Reports

The Coorong, Lower Lakes and Murray Mouth (CLLMM) region covers approximately 142,500 hectares and includes areas of local, national, and international significance. The CLLMM region is highly vulnerable due to the combined pressures of upstream water regulation, inherent ecological sensitivity and climate change. Climate change impacts will be increasingly realised as declining freshwater inflows, increasing ambient temperatures, and rising sea levels pose significant challenges to the region. The region is ecologically, culturally, and socially important which makes the CLLMM a highly valued and dynamic landscape involving diverse stakeholders, including First Nations community and organisations, community and community organisations, researchers, industry, and management agencies. Increasingly, incorporating local knowledge through community consultation is recognised as essential to effective environmental research and management. To support shared contributions that guide the future direction of knowledge generation in the region, we applied an inclusive two-phase horizon scan methodology to engage a diverse range of stakeholders. Phase 1 involved a survey (N=639) capturing perspectives on key challenges, opportunities, and novel unasked questions. Phase 2 consisted of a stakeholder workshop to identify priority issues through deeper analysis of the survey data. Results from the survey highlighted a wide range of themes, reflecting the region’s complexity. The outcomes of the horizon scan readily synthesise into five main pillars: Water Security and System Management, Climate Change and Future Extremes, Ecosystems, Biodiversity, and Fauna, Environmental Protection, Rehabilitation, and Restoration, and Human Systems, Governance, and Community Engagement. The pillars reflect the top five challenges, opportunities and novel unasked questions of the horizon scan. The identified pillars direct research that will enhance predictive understanding through forecasting and scenario planning. Additionally, they improve the evidence-base for biodiversity conservation and restoration actions. Further, the pillars support better governance and collaboration, strengthened education, science communication, and community-based involvement. A focus on this research direction will generate knowledge to support integrative and adaptive management under uncertainty that can translate into robust decision-making and action to shape the future of the CLLMM region.

Historical foredune and beach profile data for the Victor Harbor to Kingston region collected by the Department of Environment and Water, together with LiDAR datasets from 2008 and 2018, were analysed to assess the magnitude of topographic change and to investigate potential shoreline responses to sea level rise. The analysis shows that beach–dune systems in the region exhibit high spatial and temporal variability, with profiles indicating accretion, erosion, or relative stability depending on location. While a small number of sites, such as Victor Harbor and Cape Jaffa, show persistent erosional behaviour and very few (e.g. Goolwa) display accretion, no consistent long-term erosion trend attributable to sea level rise is evident over more than 40 years of observations. Instead, short- to medium-term fluctuations driven by storm-induced erosion and subsequent accretion during calmer wave conditions appear to dominate the record, masking any potential sea level rise signal.

Revegetation, human assisted regeneration and care of remnant vegetation have been occurring for many decades, and are part of the social fabric of the Coorong, Lower Lakes and Murray Mouth (CLLMM) region. Recent ecological surveys of remnant ecosystems and areas that were revegetated fifteen years ago have demonstrated multiple benefits of revegetation at the landscape scale for plants, birds and overall ecological health. Surveys of landholders and practitioners involved in revegetation have yielded additional information on revegetation success factors and key considerations for adapting revegetation techniques to a changing climate. The results of these surveys were presented at a workshop in March 2026 that brought together First Nations, scientists, local practitioners and community members. They distilled the key findings of the surveys, reviewed draft revegetation principles and considered what an adaptive management framework for future revegetation and human-assisted regeneration might need in terms of guiding principles, a community of practitioners, funding continuity and monitoring for evaluation. Key reflections of the workshop included the importance of: · Understanding your site in terms of regional context and changing climatic conditions, · Working with neighbours and other communities to connect vegetation across the landscape, · Incorporating cultural knowledge, including cultural burning, into best-practice to achieve the best biodiversity and ecological function outcomes, · Adaptive planning that uses different species and/or techniques over time, · Long-term funding to enable planting when and where conditions are suitable, and · Monitoring and sharing results of success and failures to continuously improve our practices. This report is a snapshot of practitioner and researcher responses to the results of the surveys and the resultant discussions around principles for future revegetation in the CLLMM region. The next steps needed to develop a regional revegetation framework are outlined and focus on development of documented principles and practices, formalisation of demonstration sites and deeper examination of the plant species-specific climate projections to ensure the most appropriate species are being planted. This workshop was a significant step in the pathway towards a co-designed future revegetation framework that is tailored for the CLLMM region and based on decades of experience and the latest research.

The Coorong, a Ramsar‑listed coastal lagoon of ecological, cultural and economic importance, is undergoing change as a result of climate‑driven shifts in freshwater inflows, temperature, sea level and extreme weather events. Phytoplankton are important bioindicators of these changes due to their rapid turnover rates and are foundational to the functioning of the Coorong’s food web. This report synthesises 16 years of phytoplankton and environmental data (2007–2023) to examine how climate‑mediated flow variation shapes the Coorong’s microalgal communities, supporting a predictive framework to understand future environmental trajectories and phytoplankton responses under climate change. Through an integrated analysis combining long‑term monitoring, statistical modelling, machine learning and habitat‑based ecological characterisation, this study delivers a comprehensive assessment of how climate variability affects phytoplankton community dynamics and harmful algal bloom (HAB) risk in the Coorong. A full range of hydrological conditions were captured in this study, from the Millennium Drought (extreme dry) to a large River Murray flood (extreme wet). These contrasting climate periods produced dramatic shifts in barrage flows, water levels, salinity, temperature and nutrient concentrations, which in turn restructured phytoplankton abundance, diversity and community composition. The Coorong’s environmental conditions significantly differed across flow periods. During the dry and extreme dry periods, freshwater inputs declined lowering water levels and increasing salinity to levels exceeding 190 PSU in the South Lagoon. Wet and extreme wet periods reversed these conditions, producing rapid freshening, increased hydrological flushing that removed nutrients and salt from the system and increased water levels, that further diluted salt and nutrients. Phytoplankton communities demonstrated strong, statistically significant responses to these changes, with significantly lower abundances under both extreme wet and dry conditions, but higher richness under wetter conditions and higher evenness during drought. Across an ensemble of analytical approaches, including multiple correlation analysis, ordination, distance‑based linear modelling and generalised additive models, salinity and water level emerged as the dominant drivers of phytoplankton abundance, diversity and community structure. These variables are tightly coupled and both controlled by freshwater inflows. Higher water levels and lower salinities promoted Cyanobacteria and Chlorophyte abundance. Conversely, increasing salinity altered species composition across all taxonomic groups, with increasing dominance of Diatoms and Dinoflagellates. Other important secondary drivers of phytoplankton community dynamics included temperature, distance from the Murray Mouth (representing hydrodynamic and salinity gradients) and nutrient concentrations (particularly NOX and PO₄), although their influence was weaker and more variable across statistical models. To characterise responses to hydrological change, phytoplankton communities were classified into six salinity‑derived habitats spanning freshwater (H1) to extreme hypersalinity (H6). Community composition, abundance and diversity significantly differed between habitats. Key patterns included: · Freshwater and low‑brackish habitats (H1–H2) had the highest richness but lower evenness, driven by Cyanobacteria and Chlorophyte dominance, particularly under wetter periods. However, H2 demonstrated the most equal representation of all taxonomic groups, · High‑brackish to marine conditions (H3) displayed moderate diversity and high evenness and were dominated by Diatoms and Dinoflagellates, · Hypersaline habitats (H4–H5) supported very high picophytoplankton abundance and Diatom dominance, and · Extreme hypersaline conditions (H6) had the lowest richness but highest evenness and were dominated by Diatoms and Dinoflagellates with limited representation from other groups. These habitat‑based community descriptions provide a strong foundation for forecasting future ecological states using hydrological model outputs that predict salinity. A total of 106 potentially harmful algal bloom forming species (HABs) were identified across the study period, including 82 toxin-producing species. Most HABs occurred in low‑salinity habitats (H1–H2) in the North Lagoon, especially during the post‑drought wet period in 2012. Although HAB events were generally infrequent and short‑lived, two notable bloom events occurred: 1. A Cyanobacteria bloom from January to June 2012 in the North Lagoon consisting of multiple species, though dominated by Aphanocapsa sp. and exceeding medium to high risk thresholds, and 2. A Dinoflagellate bloom during the extreme dry period, where Alexandrium spp. reached action‑level abundances across all sampling sites. Despite overall low HAB prevalence, the action-level abundances of Alexandrium species capable of producing toxins warrants ongoing vigilance, particularly under future climate scenarios that may increase the frequency and intensity of low‑flow, high‑salinity conditions or sharp nutrient pulses. An extreme gradient boost (XGBoost) machine learning model was used to predict HAB species abundance from environmental variables. The model performed strongly across much of the dataset, explaining 77% of the variation in HAB abundance, with a normalised root mean square error of 5.7%. The model’s predictive performance declined under very high observed HAB abundances (> 1.0 x 108 cells L-1), suggesting that extreme bloom events are harder to predict due to their rarity and non‑linear ecological triggers. SHapley Additive exPlanations (SHAP) values were used to quantify each environmental predictor variable’s contribution to the variation explained by the model. Salinity was revealed as the most influential predictor, aligning with results from other analyses, with higher salinity strongly suppressing HAB formation. pH was the second most important variable, exerting mostly negative effects on HAB abundance. NOX and distance from the Murray Mouth were moderate predictors linked to nutrient supply and spatial-chemical gradients, with NOX exerting a positive influence on HAB formation, while HAB abundance declined with distance from Murray Mouth. The XGBoost model was developed as a tool to better understand the broad context of harmful algal proliferation in the Coorong, but not to be used as a primary method for risk assessment. However, this model has the potential to be further developed to predict the abundances of individual species that have defined cell count risk thresholds and pose a significant threat to the Coorong. Climate change projections for the Coorong predict continued declines in freshwater inflows, increased air and water temperatures, higher variability in droughts and floods and increasing marine influence with sea-level rise. Under future conditions, the Coorong is expected to experience more frequent and prolonged hypersalinity, particularly in the South Lagoon, resulting in a decline in low‑salinity habitats (H1–H2) that currently support higher species richness and Cyanobacteria and Chlorophyte diversity and abundance. Picophytoplankton, Diatoms and Dinoflagellate abundances are predicted to increase, with decreasing species richness as hypersaline habitats (H4–H6) expand. Reducing species richness and the decline of several taxonomic groups will impact the food web, affecting trophic transfer efficiency. Increasing picophytoplankton dominance will increase turbidity, reducing submerged macrophyte habitat with further consequences for the Coorong’s biodiversity. Increasing frequency and intensity of drought increases the vulnerability of the Coorong to toxin-producing Dinoflagellate HABs. Without sufficient freshwater inflows, the system risks declining to a permanent degraded state that resembles the end of the Millennium Drought (2007–2010). To maintain a healthy phytoplankton community and Coorong ecosystem, the following recommendations are outlined: 1. Maintain and enhance freshwater flows to preserve low‑salinity habitats critical for phytoplankton diversity, HAB mitigation and hydrological flushing to limit picophytoplankton dominance and maintain water clarity, 2. Implement regular and continuing phytoplankton monitoring to track changes in phytoplankton communities across varying flow periods, detect early HAB signals and improve predictive modelling of phytoplankton dynamics. It is recommended that this monitoring includes testing algal-produced toxin levels, 3. Incorporate phytoplankton community responses to coupled hydrodynamic–biogeochemical-ecological models predicting salinity, water level, temperature and nutrient inputs to capture the spatiotemporal dynamics of the Coorong, 4. Refine machine learning models predicting HABs by further refining model hyperparameters and incorporating additional variables and species‑specific predictors to improve bloom detection, particularly under extreme abundances, 5. Investigate species interactions and grazing dynamics, including co‑occurrence networks, which strongly influence phytoplankton community composition, an Strengthen HAB risk frameworks by developing species‑specific thresholds for the Coorong and integrating outputs into management response protocols.

Freshwater mussels are integral to freshwater biodiversity and provide critical ecosystem services. As filter feeders, they are ideal indicators of water quality and ecosystems health. Globally, human modification of aquatic ecosystems threatens freshwater mussel populations. The Coorong, Lower Lakes and Murray Mouth (CLLMM) region is home to the floodplain mussel (Velesunio ambiguus). Freshwater mussels are of cultural importance to First Nations in Australia, including Ngarrindjeri people of the CLLMM region who know freshwater mussel as Lokeri (Loker-engk for two mussels; Lokerar for three or more mussels). Forgotten caches of Lokeri dated to over 8000 years old have been found on Ngarrindjeri Country thereby demonstrating its use as a food source. A greater understanding of Lokeri on Ngarrindjeri Country will provide essential knowledge to address cultural considerations and the ecological management of the species. The citizen science ‘muscles in the mud’ project was sparked by community interest in the contemporary status of Lokeri in the Lower Lakes, where it was very abundant up until the early 2000s but disappeared by 2009 during the Millennium Drought. The first aim of the project was to connect with community to discuss project objectives, identify potential survey sites and increase awareness of Lokeri. The second aim was to conduct a widespread survey of Lake Alexandrina and Lake Albert to identify if and where Lokeri may be present. The third aim of the project was to examine shells of Lokeri collected from the Lower Lakes to compare three approaches to determining age and growth (counting growth increments from the umbo section and from the full cross-section, and counting external growth interruption lines). In November 2024, more than 50 members of the Ngarrindjeri community attended two yarning circles held in Raukkan and at Point Sturt. The lead researcher presented the idea for a Lokeri project that included a survey where community members could be employed to participate in field and laboratory work. The events provided a successful way to inform community of the intention to conduct a survey on Ngarrindjeri Country and the opportunity for people to participate. After the yarns, Community members entered the water, searched for Lokerar and shared knowledge across generations. This work supported both the collection of information and the continuation of cultural practice. Many not having been in the water for years and feeling connected to the water again after being disconnected for so long. Many reporting how their mi:wi (spirit) felt happy again. In December 2024, 34 sites were surveyed in the Lower Lakes in lake-edge habitats known to be preferred by Lokeri. Lokeri presence and abundance at each site was measured using three adjacent 10 ×10 m quadrats in a randomly chosen location that were accompanied by a wider general search up to 50 m from shore and approximately 50 m either side of the quadrats. Numbers of live Lokeri and empty shells were recorded and each live Lokeri was measured for a range of morphometric parameters including length, height and width. A total of 76 live floodplain mussels and two river mussels (Alathyria jacksoni) were recorded from 9 and 1 of the 30 sites in Lake Alexandrina, respectively, but neither species was detected in Lake Albert. The quantitative surveying revealed low abundances across all sites, with temporal comparison from surveys conducted 45 years prior at Point Sturt, Lake Alexandrina, indicating the current population is

The Coorong Lower Lakes and Murray Mouth (CLLMM) region supports more than 35 freshwater fish species, including several threatened small-bodied species. Already at risk, small-bodied fishes were severely impacted by the prolonged Millennium Drought (2001–2010) and will be vulnerable to the impacts of environmental change in the region. Some of the most affected fish species were the southern pygmy perch and Yarra pygmy perch. A range of conservation actions have been implemented in the attempt to recover these two species. Among these actions are improved water level management, habitat restoration, alien species control, and translocations to reestablish resilient, connected populations to help secure the long-term survival of the species. Despite 17 years of interventions, both species remain precarious, and key questions remain about how to achieve self‑sustaining populations. To help inform future management of wild and ex situ pygmy perch populations, reintroduction ecology, and the use of water for the environment, this project built on ongoing collaborations and conservation actions, and used 15+ years of data on southern pygmy perch from the CLLMM and Eastern Mount Lofty Ranges (EMLR) regions, modelling, otolith aging, and field experiments to investigate how life history processes (e.g. reproduction) and population demographics are associated with biotic and abiotic variables. Population modelling aimed to determine trends (changes) in southern pygmy perch abundance and recruitment over time (phase 1), and the drivers of these trends (phase 2). Broadly, relative abundance of southern pygmy perch declined in the EMLR and increased in the Lower Lakes over the study period (2007–2025). These findings indicate that the effects of environmental change may be evident in the EMLR population, with fish abundance declining in a continuing drying climate and limited water resource system. Although the Lower Lakes population underwent considerable disturbance during and after the Millennium Drought, the continuing positive trajectory of this population indicates this region may confer resilience to this species in the face of environmental change. In the EMLR, however, the southern pygmy perch population is likely to continue to decline and urgent intervention is required. The second phase of characterising trends in southern pygmy perch populations in the EMLR and Lower Lakes was to determine which environmental variables may be driving the population trends using empirical and model methods. In the EMLR, at the regional scale, modelling of the relative abundance of southern pygmy perch, in relation to potential regional environmental drivers, revealed that the Antarctic Oscillation (AAO), with a time lag of two years, was the most influential driver, with empirical analysis showing a positive AAO drove a decrease in southern pygmy perch and that this relationship strengthened after the Millennium Drought (2009). This result highlights the compromised long-term sustainability of southern pygmy perch, and other small-bodied fish species in the EMLR under current and future changing climates where positive AAO conditions will be more common. In the Lower Lakes, modelling of the relative abundance of southern pygmy perch in relation to regional environmental driver data revealed that mean lake level, with a lag time of six months (previous September), was found to be the most influential driver with a positive relationship, where elevated lake water levels promote increased abundance. As the key driver of relative abundance of southern pygmy perch in the Lower Lakes, the importance of lake water level management, via River Murray flow and barrage operations, is paramount. The optimal conditions to promote recruitment in Lower Lakes southern pygmy perch populations is approximately a 0.8 m Australian Height Datum (AHD) lake water level in September. In both the EMLR and Lower Lakes, the density of aquatic macrophytes present was found to be the most influential site level, local driver of southern pygmy perch relative abundance compared to the other suite of drivers tested. A strong positive relationship was found where increasing macrophyte density drove an increase in southern pygmy perch abundance. These modelling results, of site-scale drivers of southern pygmy perch abundance, led to a field experiment to investigate how aquatic macrophyte density may influence the recruitment and abundance of southern pygmy perch in the Lower Lakes. Although Southern pygmy perch were not recaptured during field experiments, results revealed early-stage juveniles from other native fish species were only found in high vegetation enclosures, and that most adult native fishes were found in high vegetation enclosures. No significant differences were observed between water parameters in high and low vegetation enclosures; thus, water physico-chemistry may not be a contributing factor to variability in fish abundances between treatments. The use of otoliths to gain knowledge about southern pygmy perch can help inform how hydrological manipulations of lake water levels will influence the timing of breeding and the outcomes of recruitment (e.g. growth rates). This study is the first to provide credible age estimates of the Vulnerable MDB population of southern pygmy perch. Daily increments were found to be interpretable in most southern pygmy perch up to ~50 mm total length. Daily age estimated hatch dates were predominantly in spring and summer. September and December were the most frequent months of hatching, closely followed by January. Quantification of hatch dates, estimated from age, are potentially informative for the conservation of southern pygmy perch particularly in the Lower Lakes. For example, knowing the time of spawning can inform the precise timing of environmental watering interventions to maximise reproduction and recruitment. This type of watering intervention is frequently undertaken by the Department of Environment and Water (DEW). The modelling chapter of this report shows the optimal conditions to promote recruitment of Lower Lakes southern pygmy perch populations is approximately 0.8 m AHD lake water level in September. The hatch dates in the current study were most numerous in September, which suggests the optimal conditions revealed by the model are strongly related to spawning and recruitment. Together, these findings provide a clear evidence base to guide future conservation actions for threatened small‑bodied fish in the CLLMM region