Freshwater Research Centre

Freshwater ecosystems are the most threatened on Earth, with many species facing extinction. The Clanwilliam sandfish ( Labeo seeberi ) is South Africa's most threatened migratory freshwater fish and is endemic to the Olifants–Doring River system in the Cape Fold Ecoregion. Non‐native fish predation and river desiccation have caused a recruitment bottleneck, severely compromising juvenile survival and resulting in a declining population of aging sandfish. The Saving Sandfish Project launched an emergency head‐start intervention in 2020 to reduce extinction risk. We (1) rescued juvenile sandfish from drying pools in a key spawning tributary (the Biedouw River); (2) relocated them to 6 off‐stream reservoirs; and (3) released reservoir‐reared sandfish back into their natal river once large enough to evade non‐native fish predation. Here, we estimate survival in the reservoir environment, evaluate return rates relative to wild run size, and assess the probability of return based on conditions at release. Between 2020 and 2022, we stocked 33,391 juvenile sandfish into the 6 reservoirs. After 1 year, the estimated survival rate at one reservoir was 0.679 (range based on 95% CI: 0.385–0.973). Release and return results are presented only for the first (2020) rescue cohort. In 2021, we released 1277 sandfish from 2 reservoirs into the Biedouw River, comprising 16.6% of the 2020 rescue cohort. Mean size at release was 169 mm (SE 0.6) total length. Of those released, 994 were PIT‐tagged. A total of 77 PIT‐tagged sandfish were recorded during the 2022 spawning migration—a return rate of 7.7% of tagged releases in the first year of returns. Size of fish and distance from the Doring River at release were significant predictors of return probability, with larger fish released further from the Doring experiencing a higher probability of return. This program serves as a model for the conservation of freshwater fish where there is an imminent and high risk of extinction.

In South Africa, freshwater habitats are among the most threatened ecosystems, and freshwater fishes are the most threatened species group. Understanding patterns in freshwater fish diversity, threat, invasion, and protection status are vital for their management. However, few studies have undertaken such analyses at ecologically and politically appropriate spatial scales, largely because of limited access to comprehensive biodiversity data sets. Access to freshwater fish data for South Africa has recently improved through the advent of the Freshwater Biodiversity Information System (FBIS). We used occurrence records downloaded from the FBIS to evaluate spatial patterns in distribution, diversity, threat, invasion, and protection status of freshwater fishes in South Africa. Results show that record density varies spatially, at both primary catchment and provincial scales. The diversity of freshwater fishes also varied spatially: native species hotspots were identified at a provincial level in the Limpopo, Mpumalanga, and KwaZulu-Natal provinces; endemic species hotspots were identified in the Western Cape; and threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Non-native species distributions mirrored threatened species hotspots in the Western Cape, Mpumalanga, Eastern Cape, and KwaZulu-Natal. Some 47% of threatened species records fell outside of protected areas, and 38% of non-native species records fell within protected areas. Concerningly, 58% of the distribution ranges of threatened species were invaded by non-native species.

Invertebrates are often used as indicators of ecosystem health. In community ecology, the use of organism traits (e.g. behavioural, biological or ecological) can be of value in relation to impact diagnosis and assemblage prediction. It has also been recognised that certain traits are related to ecosystem function, and their use in biological monitoring provide insights into ecosystem functional responses to stressors. However, the paucity of trait information and non-availability of a local trait database for southern African invertebrates impede progress in using this approach for biological monitoring. To address this critical gap, we compiled an updateable trait database for southern African freshwater invertebrates. The database contains information on 40 trait categories and 204 trait attribute/modalities. Of the 40 trait categories included in the database, 12 are biological, 12 are behavioural, and 16 are ecological preferences. The database is designed to accommodate taxonomic flexibility. In this regard, trait information is entered at multiple taxonomic levels: family, genus, and species, allowing researchers working at different taxonomic resolutions to retrieve relevant information. While there are still gaps in the database, this effort represents the first attempt to synthesise available trait information on southern African freshwater invertebrates.

The Ecological Reserve (environmental flows) as defined under the South African National Water Act 36 of 1998 was designed to equitably manage water for river sustainability while maximizing economic and social welfare. We investigated the climate change impacts on the Ecological Reserve targets for a seasonal river in an agricultural catchment in the Western Cape region using the Habitat Flow Stressor Response method (which integrates hydrology, hydraulics, water quality, and ecological data) under projected climate scenarios (2041–2070). Current Ecological Reserve model outcomes for 3 sites on the Doring River were compared with the future hydrology using Global Circulation Models associated with four Representative Concentration Pathways (RCP 2.6–8.5). Climate predictions reflected reduced future flows, but the uncertainty band of predicted future flows overlapped with present day flows. Flood flashiness following heavy rains and the increased length of dry periods that are predicted would both contribute to increased erosion and geomorphological degradation, and further compromise biodiversity including the endangered fish populations and threaten both freshwater and estuarine ecosystems downstream. Salinity variation is predicted to increase in future leading to increased seasonal salinity stress and reduced use of abstracted water. We interrogate various options for mitigating the impacts including augmenting dry season flows, developing on-farm, catchment-scale, and strategic water resources management, and removing alien vegetation.

Human activities have cumulatively altered natural thermal regimes, with impacts and occurrences of extreme events amplified and exacerbated by global climate change. This leads to cascading ecological impacts in river systems. This paper translates knowledge generated over more than ten years of thermal research in South Africa into a protocol for establishing environmental water temperature guidelines for perennial rivers in South Africa. Tools and protocols for generating thermal guidelines reflecting seasonal variation and daily ranges, setting ecologically relevant thermal targets, and approaches for incorporating water temperature into management plans are presented. Tools include a spatial (thermal) framework within which air-water temperature models are applied and reference thermographs are generated; national maps of system resilience and air-water temperature model accuracy; a database of variables likely to indicate system resilience and model accuracy; innovative tools for generating thermal metrics and thermographs; a screening process to assess thermal risk; and an evaluation process to assess thermal change based on deviation from reference or expected thermal conditions. The importance and value of thermal data was recognised by the freshwater community and collection of water temperature data strongly endorsed. Future rollout of a water temperature-monitoring programme for South Africa needs to be prioritised.

Freshwater fish are in decline worldwide as a result of introduced non‐native species, impoundment, water quality changes, over‐abstraction, and climate change. The Clanwilliam sandfish Labeo seeberi is an endangered migratory cyprinid endemic to a single river system in South Africa's Cape Fold Ecoregion. It has declined across its range and persists as fragmented populations in the Doring River system. One of the last recruiting populations occurs in the Oorlogskloof River, where three non‐native fish species are present: smallmouth bass Micropterus dolomieu , bluegill sunfish Lepomis macrochirus (both alien and invasive), and banded tilapia Tilapia sparrmanii (extralimital). Impacts of these non‐natives, together with climate change, may pose a serious threat to this important sandfish population and to other cohabiting native fish species. A 6 year data set, collected over 9 years and spanning 25 km of the Oorlogskloof River, was analysed to characterize spatio‐temporal variation in sandfish abundance and size structure and to evaluate the relative impacts of biotic and abiotic factors on population trends. Sandfish experienced a 92.6% decline in relative abundance from 2013 to 2018, driven by a 99.6% decline in young‐of‐the‐year individuals. A combination of extreme rainfall events and drought appear to have played a key role in the decline and subsequently prevented recovery. Small sandfish (≤200 mm) were almost entirely absent from the centrarchid‐invaded section of the Oorlogskloof but were relatively abundant where these centrarchids were absent, suggesting a strong adverse impact of these non‐native species. Banded tilapia co‐occurred with sandfish without any apparent adverse impacts on the relative abundance or size structure of sandfish. Improved water resource management and preventing the further spread of non‐natives must be conservation priorities. Localized eradication of non‐native species must also be considered to reclaim habitat and restore connectivity. Translocations may be required to prevent species extinctions.

Access to long-term biodiversity datasets is vital for monitoring, managing and protecting freshwater ecosystems. Detecting critical ecosystem changes, such as losing unique biodiversity and ecosystem services, is dependent on access to data. A wealth of biodiversity data exists for river ecosystems in South Africa, but an operational information system to access these data is currently not available. This gap is the result of limited capacity for managing freshwater biodiversity data, with existing systems isolated, difficult to access and not well maintained. To address this knowledge gap, the Freshwater Biodiversity Information System (FBIS) has been developed. The FBIS is a powerful, visual, data-rich information system for hosting and serving freshwater biodiversity data. It serves as a platform for the inventory and maintenance of data, thereby facilitating the evaluation of long-term change in river biodiversity and ecosystem condition, and guiding future monitoring strategies and management decisions. System design and functionality was strongly informed by data and reporting needs of key end-user groups, including water resource managers, biodiversity and conservation managers and planners, scientific researchers, and environmental consultants. Future expansion aims to increase the diversity of data accessed, data flow, geographic coverage and strategically embed FBIS into South Africa’s main freshwater decision-making pipelines.

As the impacts of the anthropocene intensifies, there is an increasing need to understand how these changes affect both daily and sub‐daily stream flow variability, timing and flow quantities, as these are some of the most influential drivers of spatial and temporal dynamics of stream biota. In this paper, long‐term changes in flow patterns of a strategic water source area (Luvuvhu Catchment) in an arid region of southern Africa were quantified, focusing on the relation between daily and sub‐daily flow and its potential impact on fish biota of the catchment. Long‐term temporal trends in stream flow were modelled using Generalized Least Squares (GLS), while sub‐daily and daily mean flow of the same stations were compared using a suite of metrics. Periods of similar stream flow patterns were identified using K‐means cluster analysis. A spreadsheet rule‐based model was developed linking fish communities to streamflow patterns providing a predictive framework for fish assemblage responses to stream flow classes. Long term reduction in flow in the Luvuvhu Catchment has a strong seasonal component, with significant decreases during the wet season, not linked to long‐term rainfall patterns. The flow regime of the Luvuvhu river system has become more variable over time. Several sub‐daily flow metrics were positively related to daily flow metrics. Oscillating flow conditions and the loss of intermediate flow states may permanently exclude certain fish flow guilds. However, temporal partitioning is only evident when sub‐daily metrics are considered, highlighting their importance for assessing ecological resilience.

• This study aimed to develop an integrated analytical framework to identify candidate sites for surface water protection that is applicable at broad scales and in data scarce regions, using Zambia as a case study. • In the Zambian Water Resources Management Act of 2011, Water Resource Protection Areas are defined as areas where special measures are necessary for the protection of a catchment, sub-catchment, aquifer, or geographical area. Three specific selection criteria are listed for the definition of Water Resource Protection Areas: (i) areas of high importance in providing water to users in a catchment; (ii) aquatic areas of high ecological importance; and (iii) areas that are particularly sensitive to human impact. • In this project, each sub-catchment and river reach of Zambia was characterized for their importance regarding these three criteria. ‘Water provisioning’ was assessed by analysing patterns of runoff generation and human water use; ‘aquatic ecological importance’ was determined by conducting a freshwater biodiversity and ecosystem assessment using a systematic conservation planning approach; and ‘sensitive areas’ were identified by quantifying erosion potential and sediment transport. The work was supported by an assessment of free-flowing rivers in Zambia, i.e., those rivers where aquatic ecosystem functions and services are largely unaffected by changes to fluvial connectivity through dams and other infrastructure. • Highly ranked sub-catchments were found in the Liuwa, Barotse, and Bangweulu floodplains and wetlands, and in the headwater regions of the upper Zambezi, Kafue, Chambeshi/Luapula, and Tanganyika catchments. The Luangwa was identified as the highest ranked candidate river for protection within Zambia. • The resulting maps, data, and methods are intended to support national-scale efforts to prioritize areas for surface water protection, identify catchments and rivers with high conservation value, optimize decision making for infrastructure development, and inform concerted strategies to maintain and restore freshwater ecosystem services in Zambia.

• Although the network of national parks in Zambia offers a degree of protection for freshwater diversity, the protection status of numerous systems outside of these parks requires further action. The biodiversity associated with its freshwater systems, both lotic and lentic, is unique, covering a climatic gradient from tropical to subtropical across the Zambezi and Congo basins. Recent Zambian legislation allows for the delineation of water resource protection areas (WRPAs), with one of the criteria being that they include aquatic areas of ecological importance (AEIs). • In this study, a systematic conservation planning approach was used to identify aquatic AEIs objectively. Importantly, the approach included a rigorous and iterative stakeholder engagement and review process. • The conservation planning software marxan was chosen because of its ability to integrate upstream–downstream connectivity. In total, 5,671 planning units (sub‐catchments with an average area of approx. 14,000 ha) were populated with 77 biodiversity features: data were drawn from a wide range of sources, and included fishes, semi‐aquatic mammals, molluscs, amphibians, and ecotonal physiographic features, such as waterfalls. Sub‐catchments were preferentially chosen using a combination of area‐ and distance‐weighted boundary costs. • The final solution highlights critical clusters in each of the major freshwater ecoregions in Zambia, with all conservation targets being met. Results show that although the existing protected area network also coincides with identified aquatic AEIs, approximately 80% of all aquatic AEIs fall outside of formally protected areas. • The outcomes of this process serve as one of three prioritization layers (the other two being water provision and sensitivity to human impacts) that are integrated in a larger study to select and prioritize WRPAs.

Benthic macroinvertebrates are commonly used to assess water quality and ecological condition of aquatic ecosystems and they form the basis of several biotic indices. Many of these biotic indices are based on rapid bioassessment protocols (RBP). The first RBP based on macroinvertebrates, developed in Africa in the early 1990s, was the South Africa Scoring System (SASS). Since then SASS has been widely used in southern Africa and beyond, and has formed the basis of several other RBPs developed in Africa. This paper explores the RBPs and associated biotic indices currently used in Africa, primarily those that are rapid, field-based with low taxonomy (mostly family level) and which rely on sensitivity weightings of individual taxa to generate three metrics for interpreting water quality and ecological condition of aquatic ecosystems. Recommendations for future regional adaptation of RBPs, including calibration, validation, and modification of RBPs and biotic indices for new regions are provided. To date, five RBPs have been developed in Africa, while some existing biotic indices have been used outside their intended regional range. Key to the efficacy of any RBP and associated biotic index is the ability to detect a water quality impact, or change in river health. Important considerations when adapting an index for a new region or country include evaluating the suitability of the sampling protocol to local river conditions, evaluating the distribution of aquatic macroinvertebrate taxa in the region, assigning sensitivity weightings to new taxa in the region, evaluating the ability of the biotic index to detect impacts, evaluating within-country spatial and temporal variability in macroinvertebrate assemblages, and developing appropriate data interpretation guidelines based on metric scores and reference conditions. Often several iterations of a biotic index are needed, with improvement in efficacy with each version, following spatially and temporally comprehensive sampling. Future RBPs developed for bioassessment of rivers in Africa will promote the protection, conservation, and management of African riverine ecosystems.

Calls for implementation of environmental flows have been growing over the past 20 years, and their implementation is now being recognized. The need for such assessments to occur in conjunction with maintenance of environmental water temperatures has also been emphasized. When the costs of departures from natural thermal regimes are considered, this moves from being an academic exercise to a tangible management imperative. Pest outbreaks of aquatic macroinvertebrates typically occur when environmental conditions disproportionately and overwhelmingly favor a particular species. This has been the case for at least three major river systems of economic importance in South Africa, namely, the Orange River and its major tributary (Vaal River) as well as the Great Fish River. In these rivers, two species of pest blackfly, Simulium chutteri and S. damnosum (Diptera: Simuliidae), have become problematic following on from changes in natural flows through either impoundment or interbasin transfers. In this study, a statistically robust reference thermal condition was defined and exceedances assessed (based on a 2°C increase in water temperatures). The implications of these assessments were then applied to future possible pest blackfly outbreaks, factoring in changes in flows in response to global climate change. Results show that the current seasonal variation in the likelihood of pest outbreaks is replaced by high perpetual outbreak probabilities. Interactions between major environmental variables become synergistic, with major cost implications to regional economies. Lessons from this study can be generalized and used as a means of predicting similar synergistic effects in other aquatic macroinvertebrate disease vectors (such as bilharzia vector snails and mosquitoes) in response to global climate change.

Spatial variability in macroinvertebrate assemblages of the Okavango Delta, Botswana, was examined to evaluate differences in assemblages at a regional and habitat scale. Sampling was undertaken six times during a one-year cycle from 2005 to 2006, with 228 macroinvertebrates samples collected from different aquatic habitats in 22 sites in four study areas. Sixty-four taxa, mainly families, and >30 000 individuals were recorded. Multivariate analysis of aquatic macroinvertebrates revealed that the distribution of macroinvertebrate fauna is relatively homogenous among study regions, with some variation in number of taxa. Differences were observed in the macroinvertebrate assemblages associated with different aquatic habitats, with fauna from deltaic habitats (floating vegetation, inundated floodplain and marginal vegetation) different from non-deltaic habitats (isolated, seasonally flooded pools and isolated, temporary, rain-filled pools). Within the deltaic habitats, there were no significant differences among the habitats in terms of number of taxa and abundance, although assemblages and frequency of occurrence of taxa differed among habitats, providing evidence of habitat preferences for certain taxa. Future development of a macroinvertebrate-based bioassessment tool should account for aquatic habitat, although the tool does not need to be region specific. Temporal variability of macroinvertebrate assemblages should be examined to evaluate potential hydrological effects on the tool.

Different values have resulted in conflicts between anglers and conservation lobbies in the management of trout in South Africa. Key to the conflict is the demarcation of boundaries to areas in which brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss currently occur, or are likely to establish following stocking for angling. To provide a longer-term perspective on these areas, we developed models to link salmonid biological thermal thresholds to elevation. These, when applied spatially using a digital elevation model with a probability of occurrence model, provided the basis for estimating potentially available thermal habitat for these two cold water species. Here, we acknowledge that other variables (stocking history; river connectivity) also play a role in understanding trout distributions. Using a simple scenario of an increase in mean daily water temperatures of 2 °C, we demonstrated that both brown and rainbow trout are likely to exhibit considerable range reductions in the future. Because it is possible that these range restrictions will result in an increasing desire to introduce trout into areas above their current distribution limits for the maintenance of angling opportunities, conservation managers should prioritise these areas, with management interventions seeking to understand what will help to limit introductions.

The Cape Fold Ecoregion (CFE) is a biodiversity hotspot with high levels of endemism in its freshwater fish fauna. This study examined inter and intra‐specific variation in critical thermal maxima (TCmax) for eight native species of freshwater fish from the CFE. Cape galaxias Galaxias zebratus, Breede River redfin Pseudobarbus burchelli, Berg River redfin Pseudobarbus burgi, Clanwilliam redfin Pseudobarbus calidus and fiery redfin Pseudobarbus phlegethon were the most thermally sensitive (TCmax = 29.8–32.8°C). Clanwilliam rock‐catfish Austroglanis gilli, Eastern Cape redfin Pseudobarbus afer and Cape kurper Sandelia capensis were moderately sensitive (TCmax = 33.0–36.8°C). An increase in intra‐specific thermal sensitivity of S. capensis was observed from east to west. The results were related to in situ water temperature, which influenced TCmax for all species, suggesting that thermal history is a major driver of variation in thermal tolerance amongst populations. These thermal tolerance data for freshwater fishes in the CFE demonstrate that resilience to climate warming follows a geographical cline and that the more sensitive western species and regions are conservation priorities.

Understanding the response of aquatic organisms to elevated water temperatures offers insight into the ecological consequences of climate change on riverine species. Upper thermal limits were determined for two riverine invertebrates, the amphipod Paramelita nigroculus (Paramelitidae) and the mayfly Lestagella penicillata (Teloganodidae), in two rivers in the south-western Cape, South Africa. Limits were estimated using the critical thermal method (reflected as the critical thermal maxima—CTmax) and the incipient lethal temperature method (reflected as the incipient lethal upper limit—ILUT). Thermal signatures of these rivers were characterized using hourly water temperatures. CTmax for seasonally acclimatized and laboratory-acclimated P. nigroculus varied significantly amongst months and acclimation temperature. CTmax for seasonally acclimatized L. penicillata varied significantly amongst months, but not with acclimation temperature. 96-h ILUT values for seasonally acclimatized individuals varied significantly amongst months for both species. CTmax values, 96-h ILUT and Maximum Weekly Allowable Temperature thresholds were lower for P. nigroculus compared to L. penicillata. Seven-day moving averages of daily mean and maximum water temperatures were significantly correlated with upper thermal limits for seasonally acclimatized L. penicillata but not P. nigroculus. The proportion of time within a 24-h period that chronic thermal stress thresholds are not exceeded provides a measure of monthly or seasonal chronic thermal stress, and reflects the quantity of temporal thermal refugia for vulnerable organisms. Further testing of these relationships for other species, rivers and regions is recommended, to evaluate the potential for stream temperature averaging statistics to serve as proxies for biological thresholds.

Introduced rainbow trout Oncorhynchus mykiss have invaded many headwater streams in South Africa’s Cape Fold Ecoregion (CFE) and pose arguably the greatest threat to several species of threatened native fishes. Trout impacts in these systems appear to be density-dependent; we hypothesized that temperature is a key factor determining trout density and corresponding impacts on native fishes. We took advantage of natural spatial and temporal thermal heterogeneity in two CFE headwater streams to investigate the influence of temperature and other environmental factors on trout density and impacts on native fish assemblages. Temperature limited trout density (negative relationship) during summer surveys (hottest months), but not during spring and autumn (cooler months). During summer, the highest trout densities were recorded at sites that remained relatively cool (7-day moving average of the daily maximum temperature (Max_7) < 27 °C), while trout were generally absent from relatively warm sites (Max_7 > 27 °C). Native fish density was best explained by trout density (inverse relationship) during summer, but by other environmental variables such as habitat complexity and current flow velocity during autumn and spring. Trout distributions expand during cooler seasons when thermal heterogeneity and maximum temperatures are relatively low, but contract into thermal refugia (habitat patches that remain relatively cool) as temperatures and thermal heterogeneity increase over summer, leaving warmer habitat patches vacant and able to function as predation refugia for native fish. We hypothesize that climate warming could reduce trout density and distribution, and associated impacts on native fish, in CFE headwater streams, but may increase the potential for invasions by other warm-adapted non-native predatory fish already established in downstream river reaches in the region.