RESEARCH PAPER

 

Health assessment and restoration options for the degraded Swartkops Estuary, South Africa

 

 

JB Adams^{I, II}; V Tsipa^I; L Van Niekerk^{I, III}; NC James^{I, IV}; SJ Lamberth^{I, V}; B Madikizela^VI; T Riddin^{I, II}; GM Rishworth^{I, II}; GC Snow^I; NA Strydom^I; S Taljaard^{I, III}; DA Lemley^{I, II}

^IDepartments of Botany & Zoology, Institute for Coastal and Marine Research (CMR), Nelson Mandela University, Gqeberha 6031, South Africa
^IIDSI/NRF Research Chair in Shallow Water Ecosystems, Gqeberha 6031, South Africa
^IIICouncil for Scientific and Industrial Research (CSIR), Stellenbosch 7600, South Africa
^IVSouth African Institute for Aquatic Biodiversity (SAIAB), Makhanda 6140, South Africa
^VDepartment of Forestry, Fisheries and the Environment (DFFE), Cape Town 8002, South Africa
^VIWater Research Commission (WRC), Pretoria 0081, South Africa

Correspondence

 

 

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ABSTRACT

The Global Biodiversity Framework and UN Decade of Ecosystem Restoration have focused attention on the need for health assessments and restoration options for estuaries. This study focused on the Swartkops Estuary because of its biodiversity and socio-economic importance that are threatened by pressures from surrounding development and human activities. The 'Present Ecological State' (PES) was assessed using an estuarine health index to determine the health score of the estuary compared to historical reference conditions, using both abiotic and biotic indices. Results showed that nutrient-rich freshwater from upstream wastewater treatment works and stormwater canals has increased freshwater inflow to the estuary by 41% compared to natural, leading to eutrophication and persistent harmful algal blooms. Development and disturbance have transformed the estuary functional zone, impacting on macrophyte and bird abundances. Invertebrate bait organisms and linefish species are overexploited. As a result, the health of the Swartkops Estuary has continued its downward trajectory from 53% of its natural state in 2015 to 47% at present. This study is the first to identify potential remediation measures aimed at improving the current ecological health of the estuary. These include the removal of wastewater inputs and the restoration of salt marsh habitat, which would improve the ecological status from a largely modified to moderately modified condition. This study highlights how difficult it is to restore an estuary once deteriorated, while emphasising the need for an implemented estuary management plan with well-defined management, conservation, and restoration goals.

Keywords: ecological health, estuary health index, management, monitoring, remediation

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INTRODUCTION

Degradation of aquatic ecosystems, such as rivers and estuaries, is escalating following the intensification of anthropogenic activities (Feio et al., 2021). As a result of this, coastal systems are experiencing extensive deterioration in ecosystem health and their ability to maintain productivity and associated ecosystem services is compromised (Elko et al., 2022; Van Niekerk et al., 2022). Drivers of this degradation include urban and industrial development, agriculture, aquaculture, tourism, forestry, coastal erosion, overexploitation and climate change pressures such as sea-level rise (Beaumont et al., 2014; Van Niekerk et al., 2022). This is of concern as estuaries are ecologically important habitats that sustain and support unique biodiversity and provide humans with important services, including water purification, climate regulation, erosion control and habitat provision, and cultural benefits (Barbier et al., 2011).

The rehabilitation of rivers and estuaries is a global challenge and one that must be overcome if we aim to achieve global sustainability and water security. Indeed, the goals of the United Nations Agenda 2030 for sustainable development clearly state the necessity to decrease pollution, guarantee access to safe drinking water for all, and protect freshwater aquatic ecosystems and biodiversity (Kirschke et al., 2020; Feio et al., 2021). Target 2 of the 2030 Kunming-Montreal Global Biodiversity Framework (GBF) aims to expand conservation and restoration to 30% by 2030 (CBD 2022). The UN Decade on Ecological Restoration (2021 to 2030; United Nations General Assembly, 2021) calls for immediate action. Management interventions in the form of ecosystem restoration are often undertaken to improve the aesthetics of urban environments, implement ecological flow requirements as per existing legislation, prevent flooding of adjacent lands, or facilitate invertebrate and fish passage across barriers (Weerts et al., 2014; Van Niekerk et al., 2022). Regardless of the motives for restoration projects, it is important that ecosystem monitoring takes place to inform future actions (Ebberts et al., 2017; Adams et al., 2020). Successful estuarine restoration is complex and difficult, with monitoring to some type of 'conclusion' state important for costs and benefits to be defined (Elliott et al., 2016). A socio-ecological systems framework is recommended to guide estuary restoration (Adams et al., 2021; 2023). This study aims to inform estuary restoration in South Africa as few studies have addressed this topic.

In South Africa, researchers work across the science-policy-practice continuum, providing science-based solutions in support of ecosystem restoration through the National Water Act (NWA) (RSA, 1998b), National Environmental Management: Integrated Coastal Management Act (ICMA) (RSA, 2008), and Marine Living Resources Act (MLRA) (RSA, 1998a). The NWA requires that 'Ecological Reserves' and 'Resource Quality Objectives' be set for all water resources, including estuaries, through a process of 'Water Resource Classification' (Dollar et al., 2010) before water is distributed to other users, except for basic human needs and international commitments. In addition, the NWA requires the formation of 'catchment management agencies' (CMAs) to decentralise water resource management and allow all stakeholders to participate in this management within 9 'water management areas' (RSA, 1998b). The Estuarine Management Protocol (DEA, 2015), promulgated under the ICMA, was written in collaboration with estuarine scientists and offers a framework of standards and best practices for addressing the integrated management of estuaries, including the development and implementation of comprehensive 'estuarine management plans' (EMPs) for each estuary in the country (Adams et al., 2020). In addition, the MLRA requires management and monitoring of living resource use in the ocean and estuaries. Research and case studies are therefore needed to ensure implementation of this legislation and to provide the tools for comprehensive restoration planning (Simenstad et al., 2006; Claassens et al., 2022).

The Swartkops Estuary is nationally important due to its large size, diversity of habitats, and the high level of biodiversity it supports. Nationally important intertidal salt marshes as well as the endangered seagrass Zostera capensis are found in the estuary. The estuary is also of great social importance supporting recreational fishing, boating, water sports, and religious ceremonies (Adams and Riddin, 2020). It has been a well-studied estuary since the 1980s due to its urban location and proximity to Nelson Mandela University, formerly the University of Port Elizabeth (Olisah and Adams, 2021). This provides a rich source of available knowledge to inform a 'Present Ecological State' (PES) assessment of the Swartkops Estuary. The importance of the estuary and need for socio-ecological interventions to protect the services it provides have been recognised for decades (Heydorn and Grindley, 1986; DWAF, 1999a; Adams et al., 2019; Hartmann, 2021), yet the implementation of recommendations has been poor. The Swartkops River catchment falls within the Mzimvubu-Tsitsikamma Water Management Area and, up until March 2023, was managed by the Mzimvubu-Tsitsikamma proto-CMA led by the Eastern Cape Province Department of Water and Sanitation (DWS) (Meissner et al., 2017). The implementation of catchment-level restoration plans, in conjunction with the Swartkops Estuary Management Plan (EMP), is key to improving the health of the estuary and society (Adams et al., 2023). Some restoration activities have been attempted in the Swartkops Estuary, such as the construction of a pilot artificial wetland associated with the Motherwell Canal (Lemley et al., 2022; Fig. 1), implementation of a 'sustainable urban drainage system' on the Markman Canal (Mmachaka et al., 2023), and controlled collection and sale of bait organisms. However, the continued degradation of water quality (e.g., hypoxia, harmful algal blooms (HABs)) in the estuary (Lemley et al., 2023) highlights the limited success of these activities, partly due to poor control and enforcement by the responsible authorities (Lemley et al., 2022).

In the 2011 National Biodiversity Assessment, the health of the Swartkops Estuary was examined for the first time (Van Niekerk and Turpie, 2012; Van Niekerk et al. 2013). The PES of the estuary was assessed as a Category C (moderately modified) with a 'Recommended Ecological Category' (REC) of B (largely natural with few changes). In 2015, Van Niekerk et al. (2015) updated the earlier results applying the Estuarine Health Index (EHI), a standardised metric used to determine the condition of an estuary (Turpie et al., 2012), and the PES ofthe Swartkops Estuary declined to a D (largely-modified) with the REC re-defined as a C. The ecological health of the estuary had to be improved so that the system could continue providing ecosystem services (Adams and Riddin, 2020). It was concluded that the improvement of the estuary to a Category C could only be achieved with appropriate management interventions, based on a sound understanding of the main drivers and pressures impacting the estuary. As such, the aim of this study was to provide an updated PES of the Swartkops Estuary using the EHI and, for the first time, to use this process to identify possible restoration activities. Understanding the PES provides the point of departure for developing any management objectives related to estuary restoration. Lastly, restoration activities are provided to ensure the future health of one of South Africa's most important estuaries. This study provides a new standardised approach for future assessments of restoration scenarios and informs the protection and restoration objectives of the Global Biodiversity Framework.

 

METHODS

Study site description and available information

The Swartkops Estuary is located along the coast of the Nelson Mandela Bay Municipality in the Eastern Cape Province of South Africa (NMBM, 2023; Fig. 1). The Swartkops River catchment drains an area of approximately 1 390 km² (Baird et al., 1986). The river and estuary are 155 km and 16.4 km long, respectively, and both fall within the warm temperate biogeographic region of South Africa. The estuary is highly urbanised, with most development and residential areas located within a 15 km radius of the 'Estuarine Functional Zone' (Baird et al., 1986). The EFZ is that area occurring below the 5 m above mean sea level contour line. The Swartkops Estuary has a mean annual precipitation of 636 mm, with a natural mean annual runoff (MAR) of 56.9 x 10⁶ m³ (Reddering and Esterhuysen, 1981). The driest months are in summer, with the catchment receiving most of its rainfall in October with a smaller peak in April. Low baseflows and small floods of 40 to 80 x 10⁶ m³ distinguish the flow pattern in the basin. The largest recorded floods (120 to 160 χ 10⁶ m³) occurred in 1879, 1912, 1914, 1971, 1979, and 1981 (Baird et al., 1986; DWAF, 1994; Adams et al., 2023). Floods of these magnitudes change estuary channel migration and sediment distribution (Esterhuysen and Rust, 1987). Nyawo (2017) found that water from the Swartkops River and neighbouring Coega aquifer contributed to the Swartkops aquifer, making the aquifer vulnerable to Swartkops River pollution. Despite the importance of groundwater dynamics in the Swartkops Estuary, little is known about the influence and contribution of this water resource to the system.

The main residential areas surrounding the estuary are Redhouse Village, Amsterdamhoek, the Aloes community and Swartkops Village. Various developments have obstructed freshwater flow to the estuary from the river catchment, which include 5 causeways below Groendal Dam that act as weirs and reduce baseflow. The Wylde and railway bridges at Swartkops Village obstruct floodwaters, and saltpans at Redhouse hold back floodwaters, with restricted erosion resulting in downstream sand deposition (Adams et al., 2023). Lastly, the Settlers Bridge on the N2 national highway restricts flow to the northern bank at the estuary mouth and prevents lateral migration of the channel (Adams and Riddin, 2020).

Water quality in the lower reaches of the estuary is influenced by tidal flushing and turbulent mixing. In the upper reaches, however, longitudinal mixing and dispersion are limited by the Wylde Bridge. The Swartkops Estuary has an estimated residence time of 10 to 14 days for the region upstream of Bar None saltpan, and localised trapping of water may also occur in the estuary. As such, pollutants discharged into some regions of the estuary are likely to persist for extended periods (MacKay, 1994; Adams and Riddin, 2020). The estuary receives a significant volume of effluent from three wastewater treatment works (WWTWs) (i.e., Despatch, KwaNobuhle, and Kelvin Jones) that discharge into the Swartkops River just upstream of the estuary (DWAF, 1999a; Lemley et al., 2019; Lemley et al., 2023; Fig. A1, Appendix). The estuary is also subject to consistent discharges from untreated stormwater drainage systems (domestic and industrial), including the Motherwell Canal (Fig. 1; Fig. A2, Appendix), Markman Canal, Kat Canal, and Chatty River. These WWTWs and stormwater discharges have contributed to excessive eutrophication of the estuary, causing HABs and fish kills (Bornman et al., 2016; Adams, 2020; Lemley et al., 2023).

Organophosphate pesticides (OPPs) pose a threat to aquatic organisms in the Swartkops Estuary, potentially causing certain abnormalities (Olisah et al., 2022). The seagrass, Zostera capensis, is capable of accumulating OPPs and transporting these from the roots to their leaves (Olisah et al., 2021). A recent study by Olisah et al. (2023) found that fishes in the Swartkops Estuary are contaminated by OPPs, but at concentrations that are unlikely to have any human health consequences. However, the presence of antibiotic-resistant bacteria, antibiotic-resistant genes and carcinogens in the Swartkops Estuary pose a health risk to humans (Olisah et al., 2019; Chibwe et al., 2023; 2024). Kalinski et al. (2024) showed that Swartkops Estuary dissolved organic matter (DOM) composition was strongly impacted by features annotated as urban pollutants including pharmaceuticals such as antiretrovirals. Further research is needed to understand the influence of these pollutants on estuarine biota. It is important that pollutant loads be managed and natural habitats, such as seagrass beds, be restored to mitigate the social-ecological effects of water pollution.

In addition, the estuary experiences high fishing pressure because of its proximity to urban, suburban, and informal settlements, with an estimated total catch of 47 t per annum (Van Niekerk et al., 2022). Residents from nearby townships and informal settlements make a living by subsistence fishing and supplying bait (invertebrates) to recreational anglers. Illegal fishing, unpermitted bait collection, linefishing and gillnetting are responsible for 20% of the annual catch and increasing. Lack of monitoring of the fishery at the Swartkops Estuary has led to uncontrolled bait collection (Fielding, 2021; Simon et al., 2021). Alien vegetation is also a growing threat to the estuary's biodiversity as some of these invasive species, such as water hyacinth (Pontederia crassipes), enter a stage of exponential growth in the river/upper estuary and choke waterways (Zengeya et al., 2020; Lakane et al., 2024). Similarly, there are 5 introduced freshwater fish species in the upper reaches, and poor water quality has facilitated the proliferation of invasive alien Pacific oyster Crassostrea gigas throughout the estuary (Ellender et al., 2011; Keightley et al., 2015). This and other available information were used to assess the PES of the Swartkops Estuary.

Study approach

The PES of the Swartkops Estuary was assessed using the EHI that considers 4 abiotic drivers and 5 biotic responses, addressing the characteristics and functioning of each component, their interrelationships, and distinguishing between flow and non-flow-related pressures and associated impacts (Turpie et al., 2012; Van Niekerk et al., 2022) (Fig. 2 adapted from DWAF, 1999a). For the abiotic drivers, the components studied included hydrology, water quality, hydrodynamics (which includes mouth condition), and physical habitat alteration. In terms of the biotic components, microalgae, macrophytes, invertebrates, fishes and birds were assessed (Van Niekerk et al., 2022).

For each abiotic and biotic component, the change in condition was estimated as a percentage (0-100%) of the natural state (120 years ago, i.e., predevelopment conditions), based on the Bray-Curtis dissimilarity index (Bray and Curtis, 1957). The macrophytes are used as an example to show how the detailed scoring is completed for the biotic components of the EHI. Scores were weighted (25% for each abiotic and 20% for each biotic component) and aggregated (50:50) to provide an overall score that reflected the present health of the system as a percentage of that under natural conditions (Van Niekerk et al., 2015; Fig. 2). Individual scores were then aggregated into an overall EHI score using a scale of A to F (Fig. 2). Further details on the approach and scoring method applied are described in Van Niekerk et al. (2013; 2019a; b) and can be found in the environmental water requirement report (Swartkops EWR Report, 2021).

The assessment ofthe PES was undertaken at an estuarine specialist workshop comprising a multi-disciplinary team including both abiotic and biotic expertise with specific knowledge on the Swartkops system. Restoration activities were also identified to improve ecological health. Confidence levels for the data used in the study applied the scoring criteria presented in Fig. 2. A literature evaluation of all recent research undertaken within the Swartkops Estuary was completed, and existing datasets were evaluated to quantitatively detect any changes over time (Table 1) to inform the estuary health assessment.

A key driver in the evaluation of estuary health is understanding the past and present freshwater inflow (hydrology), as it is the modification of freshwater flow regimes that affects estuarine productivity and functioning (Van Niekerk et al., 2013; Stein et al., 2021). Monthly hydrological flows over a 90-year period were simulated using a Pitman monthly flow hydrological model (Water Resources of South Africa, 2012: WR2012, 2021). These were generated for the reference (or natural) conditions, the present state, as well as for a range of future scenarios. These simulated data sets were then used to provide monthly flow percentile distribution summaries that highlight occurrences of low flows, drought and flood events. The hydrodynamics of the predominantly open Swartkops Estuary considered changes to the estuary mouth state (closed, constricted, open, or wide open), flood inundation of the floodplain, tidal range, circulation processes, and salinity structure (well-mixed or stratified) by comparing field observations conducted prior to the construction of the Settlers Bridge at the estuary mouth to present. Water quality parameters applied in the EHI and for which reliable data were readily available included salinity, dissolved oxygen, Secchi depth (alternative to total suspended solids), inorganic nutrients (dissolved inorganic nitrogen (DIN) and phosphorus (DIP)), and toxic substances (metals and selected persistent organic pollutants (POP)) (Table 1).

The changes in hydrology, water quality, hydrodynamics, and physical habitat from natural to present were then used to score the present state for the abiotic components. A comparison of the abiotic and biotic scores between the 2015 and current assessment are presented. Available literature and data were used to determine the present species richness, abundance, and community composition of each of the 5 biotic components, with the lowest scoring of these 3 indices being used as the health score of that component (Fig. 2). Past aerial images dating back to the 1930s were used to determine the extent of natural habitat and vegetation lost in the EFZ to development and land transformation. Aerial imagery was obtained from the Chief Directorate: National Geo-spatial Information (2021). Heads up digitizing was completed for the earliest imagery (1930s to present 2015). The recent images are orthorectified and have a 50 cm resolution; these were used as the basemaps to digitize present and past habitat extent. Recent Google Earth imagery was used to assess habitat changes.

Flow scenarios

Five alternative future flow scenarios, two worst case and three restoration options, were considered to predict possible future conditions of the Swartkops Estuary using the EHI. The scenarios were as follows:

• Scenario 1: Future climate change scenario with more intense freshwater flooding. Baseflow remains similar to present due to input from the WWTWs. Floods will increase in volume and intensity, resulting in an increase of stormwater to the estuary.

• Scenario 2: Increase in wastewater input to the estuary as reflected by a growing population and increased numbers of people predicted for the year 2050. This adds baseflow and nutrients to the estuary resulting in further water quality deterioration. This scenario is a worst-case scenario where sewage spills and low maintenance of the WWTWs are expected, and no recycling or nutrient reduction occurs.

• Scenario 3 (water quality restoration): Improvement in water quality by removing the volume of wastewater from the upstream Kelvin Jones WWTW (approximately 75% of the total present WWTW input). All other pressures remain the same as the present state so that water quality restoration can be understood and quantified.

• Scenario 4 (water quality restoration): Full water quality restoration scenario - although unlikely - where all influence from upstream WWTW inputs is removed from the estuary. Some of this could be achieved through artificial wetlands and effluent recycling. Nutrient-rich baseflow input is reduced, improving eutrophic conditions. All other pressures remain as present so that water quality restoration can be understood and quantified.

• Scenario 5 (habitat restoration): Habitat restoration scenario where 10% of the supratidal habitat is restored through re-wetting the Cerebos salt marsh areas and some riparian zone improvement by removing alien plants. All water quality pressures remain the same as present so that habitat restoration can be understood and quantified.

 

RESULTS AND DISCUSSION

Present Ecological State: abiotic components

Hydrology

Persistent input of nutrient-rich freshwater from 3 upstream WWTWs and stormwater drainage systems has increased the MAR to the Swartkops Estuary, increasing baseflows by 4 to 8 times (Table 2). Under the reference condition, river inflow of less than 0.3 m³-s^-1 occurred for 55% of the time, but the increase in river flow means that flows of less than 0.3 m³-s^-1 seldom occur (99% change from natural). The dams in the catchment of the Swartkops system are relatively small and thus have little effect (15%) on both smaller floods (1:5 to 1:10 years) and major floods (1:50 years). The current MAR into the Swartkops Estuary is 80.3 x 10⁶ m³, which represents a 41% increase from the natural MAR of 56.9 x 10⁶ m³. The hydrological assessment had medium to low confidence due to the lack of a flow gauge at the head of the estuary to provide more accurate data (Tables A1 and A2, Appendix). The Swartkops River is well known for the occurrence of major floods. Historical studies estimate that the maximum flow into the estuary during a 1:100-year flood was approximately 2 500 m³-s-¹ (CSIR, 1987; Hughes, 1987). Urbanisation has been shown to create higher surface runoff, higher river discharge rates, and quicker times for floods to reach their peak (Feng et al., 2021). A key uncertainty is the hardened surfaces due to urbanisation and influence on flow.

Hydrodynamics and mouth condition

The Swartkops Estuary is permanently open to Algoa Bay, and the mouth has been stabilised by the construction of the Settlers N2 highway bridge, causing the buildup of sand and constriction of the mouth during extended periods of low river input. Low river input (<0.3 m³-s^-1) during the natural state would have resulted in well-mixed marine conditions for 55% of the time. Elevated baseflows, mouth stabilisation, and the influence of bridges have led to the complete loss of the marine state and the tidal amplitude in the lower reaches of the estuary has increased from 0.5 m to between 1.0 m and 1.5 m. Confidence in this assessment is 'medium, as this was based on observations and measured data, supported by historical numerical modelling of circulation of the system (Table A1, Appendix).

Water quality

Available water quality data for the Swartkops Estuary are extensive (i.e., since 2012) and provide a good overview of changes occurring in the system (Table 1). The estuary is typically eutrophic from the middle to the upper reaches (Adams et al., 2019). There are clear trends in DIN and DIP concentrations, increasing upstream because of inputs from the three WWTWs and diffuse runoff from the Motherwell, Markman, Kat, and Chatty catchments. An approximate increase of 85% has been recorded for both DIN and DIP concentrations in the estuary. DIN concentrations exhibited a persistent longitudinal gradient, with average surface concentrations ranging from 0.11 mg-L^-1 at Settlers Bridge to 3.35 mg-L^-1 upstream at Perseverance (Adams and Riddin, 2020). The elevated inflow from WWTWs and stormwater runoff has caused the estuary to become slightly fresher, decreasing the overall salinity in the estuary by 7% on average. There has also been an increase in toxicants, mostly due to surrounding industrial activities.

The high nutrient concentrations result in eutrophication, where persistent phytoplankton blooms are recorded, especially in the middle to upper reaches of the estuary. Hypoxia and anoxia (i.e., dissolved oxygen < 2 mg-L^-1) are frequently measured in the bottom water of these reaches, associated with the die-off and decay of phytoplankton blooms. In a recent study by Lemley et al. (2022), the Motherwell artificial wetland was deemed inefficient in reducing nutrient concentrations entering the estuary from the Motherwell Canal, thus making this an important additional source of pollution to the estuary. Essentially, the canal functions as a WWTW, which is problematic because the untreated inputs are characterised by high ammonium and DIP concentrations and represent a constant daily source of inorganic nutrients that influence the nearshore environment (Lemley et al., 2019). Confidence in this assessment is 'high' as it is based on measured data.

Physical habitat alteration

Analysis of past images dating back to the 1930s shows 882 ha loss of estuarine habitat to infrastructure, coupled with residential and industrial development (Adams and Riddin, 2020). Extensive supratidal habitat has been lost with only 50% similarity to natural. This loss is the result of development, which includes the construction of the Wylde and railway bridges at Swartkops Village, the extensive saltpans near to Redhouse Village (560 ha), and the Settlers Bridge at the mouth of the estuary. An additional 556 ha is disturbed habitat due to trampling, walkways, and urban encroachment. Confidence in this assessment is 'medium to low' as the assessment could improve if there was a recent bathymetric survey (Table A2, Appendix).

Present Ecological State: biotic components

Microalgae

The EHI considers the species richness, abundance, and community composition of phytoplankton and benthic microalgae (microphytobenthos) in the estuary. The strongest driver of change for microalgae is nutrient availability, with excess concentrations supporting the persistent, high-biomass phytoplankton blooms of HAB species recorded in the estuary (Adams et al., 2019; Lemley et al., 2023). Heterosigma akashiwo was documented as being responsible for numerous high-biomass HABs (> 100 μg Chl-a-L^-1) particularly in the mid-to-upper estuary reaches, with two mass fish mortality events associated with these events (Lemley et al., 2023). Based on these field data there has been an estimated 61% increase in phytoplankton biomass in the middle to upper reaches of the estuary from baseline/natural conditions. Field data have shown that phytoplankton blooms facilitate drastic shifts in dissolved oxygen concentrations during the bloom-decay cycle, with supersaturated surface waters typical of the bloom phase and bottom-water hypoxia characterising the decay phase (Lemley et al., 2023). From published literature for other South African estuaries (Lemley and Adams, 2020; Lemley et al., 2021; Nunes et al., 2021; Nel et al., 2023), we expect that nutrient enrichment and reduced flow variability (e.g., less frequent flooding events, augmentation of baseflows) are likely to facilitate increased abundance and reduced diversity of benthic microalgal communities due to less sediment disturbance. Contrastingly, elevated turbidity, resulting from external sources (e.g., WWTWs, stormwater canals) and in-situ phytoplankton blooms (including HABs), can result in the increased shading of benthic microalgal communities in the mid-to upper reaches, reducing abundance and diversity of these microalgal communities. The microalgal assessment had a 'medium' confidence level (Tables A1 and A2, Appendix).

Macrophytes

Mapped data showed that intertidal and supratidal salt marsh areas have decreased by 64% in extent since the 1930s (Table 3). Development and industries are the major pressures causing the loss of habitat and decline of the floodplain vegetation and supratidal salt marsh area. Aerial photographs taken in 1939 indicated that large areas of intertidal salt marsh were already lost when the Swartkops and Redhouse Villages were developed. Post 1939, smaller areas of marsh were lost to the solar salt works, the power station, the Uitenhage Road and other roads and bridges. The upgrading of road interchanges in the Fish Water Flats region led to further removal of intertidal salt marsh (Colloty et al., 2000).

Elevated nutrient concentrations and more stable flow conditions have simultaneously supported the spread of invasive alien aquatic plants such as water hyacinth in the upper, fresher, estuary reaches (Lakane et al., 2024). The increase in river inflow, nutrients, turbidity, and water hyacinth has led to the loss of seagrass in the middle/upper reaches of the estuary (Adams et al., 2023). There has also possibly been some loss in reed and sedge habitat due to increased disturbance of the riparian zone. These mapped habitat changes informed the assessment of community composition (Table 4).

The health of the macrophytes was assessed in terms of species richness, abundance and community composition (Table 5). Change in species richness was measured as the loss in the average species richness expected during a sampling event, excluding species thought to not have occurred under reference conditions (Table 5). Abundance was measured as the change in area cover of macrophyte habitats. The following was used to measure abundance:

% similarity = 100 x present area cover / reference area cover

Intertidal salt marsh, supratidal salt marsh and floodplain area values were used to measure change in abundance (Table 3). In total these habitats covered 1865.93 ha but now cover 697.64 ha, with a 37% similarity compared to reference conditions. This represents habitat lost due to development, particularly establishment of salt

pans that cover 551.2 ha. Invasive plants (terrestrial and aquatic) would not have been present in the reference condition but are now abundant in the areas quantified as 'disturbed. In addition, there have been flow and water quality-related changes. Change in community composition was assessed using a similarity index which is based on estimates of the area cover of each macrophyte habitat in the reference and present state (Czekanowski's similarity index: Σ(min(ref,pres) / (Σref + Σpres)/2) (Table 4). Disturbed and developed habitat were present as intact, mainly floodplain, vegetation in the reference condition. The overall macrophyte health score (Table 5) was the minimum score of 35 for community composition changes. The confidence in this assessment was 'high' as it was based on field studies and measured/mapped data.

Restoration of salt marsh and seagrass is important as this will increase the ability of the estuary to sequester carbon dioxide from the atmosphere, contribute to long-term carbon storage stocks, and mitigate the effects of climate change. It is estimated that salt marshes and seagrasses in South Africa store carbon at levels of 100-199 Mg-ha^-1 and 45-144 Mg-ha^-1, respectively (Raw et al., 2023). Coastal squeeze caused by rising sea levels and building encroachment is a significant danger to salt marsh habitats (Raw et al., 2021). Coastal squeeze will limit salt marsh expansion in response to sea level rise as there is little available space for inland migration (Adams et al., 2023).

Invertebrates

Invertebrates within an estuary can be subdivided into interstitial meiofauna (not typically considered in EHI assessments) and 4 prominent macrofaunal components based on dominant traits and drivers, namely: plankton, benthos, hyperbenthos, and intertidal. Each of these experience different pressures depending on their associated life history strategy and lifestyle. Sediment properties, especially granulometry and organic matter, are the primary structuring forces of benthic organisms (Teske and Wooldridge, 2003).

Additionally, the benthic and intertidal macrofauna are affected by anthropogenic pressures such as coastal squeeze, disturbance, and direct consumptive collections by recreational and subsistence user groups (Fielding, 2021). Consequently, populations of large benthic macrofauna species such as mudprawns (Upogebia africana) and cracker shrimps (Alpheus lobidens, i.e., benthic burrowers) have declined from bait-harvesting pressures. For example, using comparable sampling methods, the clearest decline has been in mud prawn abundance in the estuary, from 174 340 x 10³ total estimated organisms in 1980 to 103 611 x 10³ in 2008, and, most recently, 76 0 60 x 10³ in 2020 (Fielding, 2021). This is a loss of over half of the stock of this ecologically and economically important bait species in 4 decades (Fielding, 2021). Similar declines are apparent for species such as giant mud crabs (Scylla serrata) that are collected for subsistence (Fielding, 2021). The most substantial change compared to the reference condition is a reduction in overall abundance of benthic macroinvertebrates, especially those used for bait (e.g., sand prawns, Kraussillichirus kraussi, mud prawns, and pencil bait, Solen capensis) and subsistence (e.g., giant mud crabs) (Fielding, 2021). This loss of abundance is exacerbated by the removal of intertidal habitat through development.

Significant changes to invertebrates are also related to increased nutrient loading, changes to primary producer groups, increased prevalence of alien or invasive taxa, and pollutant loading (Lemley et al., 2023; Ndhlovu et al., 2024b). Invasion of Crassostrea gigas (Pacific oyster) is facilitated by pollution and a decline in water quality (pH increase) as well as by bridges, pipes and other hard structures on which they settle. The increased prevalence of HABs in the Swartkops Estuary is likely to have negatively impacted the species richness, abundance, and community composition of the zooplankton and hyperbenthos components, particularly in the mesohaline zone (Smit et al., 2021; Smit et al., 2023). Changes in flood states and sediment supply appear to be temporary, causing minimal disturbances to this community (McLachlan and Grindley, 1974), while the fresher conditions brought on by elevated baseflows have shifted the overall community away from a marine-dominated invertebrate fauna. An understanding of how deterioration in water quality affects macroinvertebrate communities is crucial in their use as indicators of river and estuarine health. For example, Odume et al. (2012) investigated the impacts of water quality deterioration on Swartkops River macroinvertebrate communities. At downstream river sites, the abundances of families were skewed toward the most pollution-tolerant taxa (e.g., Chironomidae, Oligochaeta, Hirudinae) and the increased dominance of Chironomidae and Oligochaeta indicated depleted oxygen and increased nutrient levels (Odume et al., 2012). The confidence in this assessment was 'medium' since there is a good baseline of information across the various invertebrate assemblages, and at least one multi-decadal dataset exists as a reference point (Fielding, 2021).

Fishes

Over 75 species of bony and cartilaginous fishes have been identified in the Swartkops Estuary (Baird et al., 1986; Edworthy and Strydom, 2016; Nodo et al., 2023; 2024; Grundlingh, 2025). The estuary consists of a variety of habitat types with extensive eelgrass Z. capensis beds that make it an ideal nursery area for fishes (Beckley, 1983; Mkhize et al., 2025). The abundance and diversity of larval and juvenile stages of estuary resident and marine species increase in spring and summer (Strydom et al., 2003; Edworthy and Strydom, 2016; Nodo et al., 2023; Grundlingh, 2025). The estuary is also an important feeding area for adult marine estuarine-dependent fishes, such as Argyrosomus japonicus (dusky kob), Pomadasys commersonnii (spotted grunter), Lithognathus lithognathus (white steenbras), Elops machnata (ladyfish), Rhabdosargus holubi (Cape stumpnose), Lichia amia (leervis), and various species of marine opportunistic Mugilidae (mullet) that are used as live bait (Marais, 1982; Baird et al., 1996; Adams et al., 2023; Whitfield and Mann, 2023; Whitfield and Smith, 2024). In addition, Swartkops Estuary is an important system for recreational and small-scale fishing; however, catches have declined over time and the size of fishes caught has decreased (Marais and Baird, 1980; Pradervand and Baird, 2002; Whitfield and Mann, 2023; Whitfield and Smith, 2024).

The reference condition for the Swartkops Estuary would have consisted of a high abundance of fishes from all trophic levels. However, due to its proximity to heavily urbanised areas, very high fishing pressure (e.g., recreational and small-scale fishing, illegal gillnetting) has resulted in significant changes to fish abundance (estimated 60% loss) and community composition (estimated 40% change), all of which impact the nursery function and trophic structure of the system (Pradervand and Baird, 2002; Van Niekerk et al., 2022). Major changes have been observed in the sizes of species and therefore the age of species commonly targeted by anglers. This is evidenced by the sizes of A. japonicus and L. lithognathus being up to 4 times heavier in records by Fitzsimons (1915, cited in Heydorn and Grindley, 1986) compared with records by Marais and Baird (1980a, b) (see Whitfield and Mann, 2023). Recent findings also illustrate the knock-on effects of overfishing on fish reproduction, where larval fish densities have decreased for common angling species, indicative of smaller adult female sizes producing smaller and fewer eggs during spawning (Grundlingh, 2025). The HABs, driven by increased wastewater inflow, with the associated fluxes in dissolved oxygen in the middle to upper regions, cause the localized loss of fish abundance and shifts in community composition of fishes in the mesohaline reaches of the estuary. Low dissolved oxygen events (< 3 mg-L^-1) in the upper reaches resulted in declines in species richness (Nodo et al., 2023). Other impacts include habitat disturbance following bait collection, the prevalence offreshwater invasive alien fish species that potentially displace catadromous species, and the unknown impact of heavy metal, organic and inorganic contamination on fish reproductive biology. Confidence in this assessment is 'high' in terms of larval and juvenile stages of fishes but adult fishes are scientifically under-sampled in contemporary studies due to the harmful effects of using traditional gill nets on populations of fishes experiencing stock collapses. Changes in angler catches were used as an indicator of change in adult fish abundance and size. Adult fish data could improve with a contemporary study on angler fish catches for comparison with historical studies.

Birds

The Swartkops Estuary is a globally recognised 'Important Bird and Biodiversity Area' (IBA). The Swartkops Estuary and the Redhouse and Chatty saltpans are considered the most important estuarine and salt-flat habitats for waterbirds along the Eastern Cape Province's coast (Martin and Baird, 1987; BirdLife International, 2021). The estuary supports up to 20 000 birds, with over 3 000 of these being annual Palearctic migrant species (BirdLife International, 2021). Most of these birds are water- and wetland-associated birds (Adams and Riddin, 2020), including the African Oystercatcher (Haematopus moquini), Greater and Lesser Flamingos (Phoenicopterus roseus and P. minor), African Spoonbill (Platalea alba), several species of kingfishers, Roseate Terns (Sterna dougallii), as well as many other waders, waterfowl and piscivorous species (Adams et al., 2023). Disturbance and habitat modification have reduced the overall waterbird abundance (Andrade et al., 2018). It is likely that the establishment of the adjacent saltpans has compensated to some degree for this, making it possible for the waterbirds to breed, feed, and roost (Martin and Baird, 1987). However, decommissioning of the Chatty and Redhouse saltpans in recent years has minimised this compensation and therefore presents an opportunity for habitat restoration to enhance localised avifauna conservation (Wasserman et al., 2022a) and increase nutrient removal (Du Toit and Campbell, 2022).

Based on studies on the influence of freshwater, sediment and habitat on invertebrates and fish (Marais, 1982), it is concluded that elevated inflow of nutrient-rich freshwater, coarsening of intertidal sediments, loss of salt marsh habitat, disturbance, increase in reeds and sedges in the upper reaches of the estuary, decommissioning of saltpans, and reduced benthic invertebrate and fish biomasses have all impacted on bird species richness, abundance, and community composition. The impacts associated with elevated turbidity, heavy metals and organic pollutants are largely unknown. An estimated 40% loss in abundance has been attributed to disturbance and habitat modification. The Swartkops Estuary has one of the best long-term monitoring datasets in terms of waterbird counts, started in the 1980s thanks to initiatives led by Dr Martin (Martin and Baird, 1987) and continued through the CWAC (Coordinated Waterbird Count) project. Confidence in this scoring is therefore deemed to be 'medium to high, with the only major source of uncertainty being that many of the impacts on the system would have been pre-1980 and therefore before any systematic monitoring efforts occurred.

Changes in estuary health over time

The current study reviewed and collated current research findings and available new data on the Swartkops Estuary and determined the trajectory of change for abiotic and biotic features (Table 6). The individual present health scores for the abiotic and biotic components were used to determine the PES of the estuary using the EHI weightings as presented in Table 6. The EHI score for the Swartkops Estuary is 47, representing a 'largely modified' estuary with a PES Category D. The overall confidence in this score was 'medium to high, derived from confidence levels assigned to most of the abiotic and biotic components. The trajectory of change is towards a highly degraded Category E system. This is evident in the decrease in EHI score from 53 to 47. This is of great concern for estuary management because, according to the guidelines for determining the REC provided by DWAF (2008), the Swartkops Estuary should be 'largely natural' with few modifications (Category B). However, due to the extent of changes the estuary has undergone and the high degree of urbanisation, the best achievable state is that of a 'moderately modified' system (Category C). A review of restoration scenarios indicates that eliminating wastewater, regulating resource use of fish and bait, and restoring riparian habitat, particularly the Redhouse saltpan, may increase the likelihood of achieving a Category C.

Future flow scenarios

The responses of the five proposed future inflow scenarios were investigated for the different abiotic and biotic components and the two worst case scenarios did not change the estuary from being a 'largely modified' estuary (Category D) (Table 7). Similarly, the estuary remained in a 'largely modified' (Category D) condition under Scenario 3, which considered the removal of 75% of the wastewater input. The estuary condition only improved to a Category C/D (moderately/largely modified) when 100% of the wastewater input was removed in Scenario 4. This indicates the significant impact that the WWTW input has on the health of the estuary as well as the influence of other multiple pressures. Besides reducing WWTW input, habitat restoration will also be needed to improve the health of the Swartkops Estuary. There was a 4-point improvement in health score from the present state (score of 47) under Scenario 5 (score of 51). Therefore, if habitat restoration (Scenario 5) is implemented in conjunction with the complete removal of WWTW inputs (Scenario 4), the estuary health score could improve to 63 (an Ecological Category of C, representing a moderately modified estuary).

Restoration options

The decline in estuary health revealed by the health assessment confirms observations made by various scholars of a deteriorating state (Pretorius, 2015; Adams et al., 2019; Lemley et al., 2023). It is evident from this health assessment that restoration interventions on the Swartkops Estuary are urgently needed. For such interventions to be effective, cooperation from all stakeholders involved in the estuary will be key. The estuary is a complex social-ecological system and restoration eflorts to improve estuary health should recognise this (Adams et al., 2023). Restoration ecology bridges the gap between application and supporting sciences, and rather than focusing primarily on ecological factors, it should include socio-ecological elements (Abelson et al., 2020; Adams et al., 2023).

From the scenarios tested, priority actions and additional restoration activities were considered for the Swartkops Estuary and are summarised in Tables 8 and 9. The poor health of the Swartkops Estuary is a result of multiple pressures that need to be addressed to improve its health. Effective water quality control measures are complicated, and it has been shown that the management of nutrients, particularly DIN and DIP, requires a multi-sectoral approach (Maier et al., 2009). The Swartkops Estuary is a nationally important site for salt marsh restoration (Adams et al., 2021) and provides an array of important nursery habitats that must be protected through fishing and invertebrate bait collecting control and the implementation of no fishing zones where juveniles and pre-spawning adults are known to congregate (Table 9). There is a proposed fishery for the invasive alien Pacific oyster (Crassostrea gigas) that could provide opportunities for ecosystem restoration and contribute to livelihoods of small-scale fishers.

Recent approaches such as natural capital accounting and its official international framework, the System of Environmental-Economic Accounting (SEEA), have created a framework to account for nature's contributions to the economy and people (Taljaard et al., 2023). Local restoration efforts could be informed by the ecosystem accounting methods, which provide detailed information about the extent of abiotic habitats, the condition of the ecosystem assets, and the services they provide. Globally ecosystems accounting has largely focused on carbon accounting, fisheries/nursery function and tourism values as key ecosystem services (Dvarskas, 2019; Gomez Cardona et al., 2023). Taljaard et al. (2023) provides a local example of how blue carbon sequestration and recreational use can be incorporated into formal ecosystem accounting processes. Information from these accounts can help prioritise, monitor and report on restoration efforts in the Swartkops Estuary.

To restore the wetland function of an abandoned commercial saltpan at Swartkops Estuary, an opportunity was identified to fill it with nutrient-rich stormwater (Wasserman et al., 2022b). In 2018, a microcosm-based study was conducted to inform a planned restoration project that aimed to simultaneously address two issues: stormwater management and saltpan abandonment (Wasserman et al., 2022b). At the end of the study, the conditions in the experiment tanks resembled those typical of primary concentration pans in saltworks. The stormwater treatments that received freshwater extracted from the Motherwell Canal reached a brackish state and the estuary treatment (initial salinity of 23) became hypersaline. Both treatments hosted a diversity of primary producers, common in low salinity ponds of saltworks (Britton and Johnson, 1987; Davis, 2000; Wasserman et al., 2022b). A main conclusion of the study was that primary producers - particularly phytoplankton and macroalgae - at the Redhouse saltpan will quickly assimilate inorganic nutrients from the stormwater, thereby relieving the Swartkops Estuary from a significant source of anthropogenic nutrient pollution (Lemley et al., 2022; Wasserman et al., 2022b). The abandoned saltpans are currently being used to receive Motherwell Canal water and act as a large pollutant filter. Ongoing monitoring is necessary to investigate the removal of nutrients by the pans, changes in physico-chemical conditions and the ecological health of the system.

 

CONCLUSION

The use of the EHI as an estuary health assessment tool enabled the identification of drivers responsible for the deteriorating condition of the Swartkops Estuary. Similarly, the index helped identify remediation measures that can be implemented to improve the health of the estuary. These measures include:

• Removal of WWTW and stormwater drainage discharges into the estuary

• Restoration of salt marsh and seagrass habitats to mitigate the effects of climate change

• Conversion of the nearby defunct commercial saltpans into extensions of the existing artificial wetland to restore waterbird habitat and filter pollution

• Reducing the pressures of bait collection and overfishing

The findings of this study highlight that, over the past decade, management and conservation efforts have failed to prevent the continued deterioration of ecosystem health in the Swartkops Estuary. There is an urgency to revisit and change the current traditional estuary management process. A socio-ecological approach presents the opportunity to engage resource users and management holistically and pragmatically. This can be achieved through the implementation of existing legislative tools, which includes the determination of an 'Ecological Reserve' and 'Resource Quality Objectives' through the process of 'Water Resource Classification' as required by the NWA, and implementation of the EMP as required by the ICMA (Adams et al., 2020). Fortunately, the Swartkops EMP has recently been gazetted and rivers within the Mzimvubu-Tsitsikamma Water Management Area, into which the Swartkops River falls, are in the process of being classified and soon to be gazetted.

Lessons learned from the study are that long-term ecological data are needed for high-confidence assessments of estuary health. Monitoring of estuaries is inadequate and does not allow for effective conservation and management. This poses a threat to the ecological health and societal benefits of an estuary. Although the assessment of estuary health using the EHI is well established, this study showed how restoration and climate-change scenarios can be considered using a similar approach. This informs the management of impacted estuaries globally.

 

ACKNOWLEDGEMENTS

The National Research Foundation of South Africa through the support of the DSI/NRF Research Chair in Shallow Water Ecosystems supported JBA and is thanked for funding (UID 84375). The Water Research Commission funded this research through Project C2020/2021-00076 'Restoration of estuaries using a socio-ecological systems framework'. Prof. Denis Hughes (Institute for Water Research, Rhodes University) completed a report on 'Hydrology and future scenarios for freshwater inflow to Swartkops Estuary' that was used to assess the Present Ecological State of the estuary. Zwartkops Conservancy members (Frank Collier, Jenny Rump, Arthur Rump, Dale Clayton, Rod Lochhead) are thanked for the ongoing collaboration and interactions on the conservation and management of the Swartkops Estuary.

 

AUTHOR CONTRIBUTIONS

All authors: Methodology of the study, data collection and fieldwork, sample/data analysis, interpretation of results, writing of the initial draft, interpretation of results, input to final draft.

JB Adams: Conceptualisation, research project management and funding.

 

ORCID

Janine Adams: https://orcid.org/0000-0001-7204-123X

L Van Niekerk: https://orcid.org/0000-0001-5761-1337

NC James: https://orcid.org/0000-0002-9472-5314

SJ Lamberth: https://orcid.org/0000-0002-4076-3622

B Madikizela: https://orcid.org/0009-0008-5037-7953

T Riddin: https://orcid.org/0000-0002-5877-3431

GM Rishworth: https://orcid.org/0000-0003-1148-0081

GC Snow: https://orcid.org/0000-0002-1316-3111

NA Strydom: https://orcid.org/0000-0003-4292-8678

S Taljaard: https://orcid.org/0000-0001-6206-8623

DA Lemley: https://orcid.org/0000-0003-0325-8499

 

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Correspondence:
Janine Adams
Email: Janine.Adams@mandela.ac.za

Received: 26 May 2024
Accepted: 16 April 2025

 

 

APPENDIX

 

Figure A1- Click to enlarge

 

 

Figure A2- Click to enlarge

 

 

Table A1 - Click to enlarge

 

 

Table A2 - Click to enlarge