Issue: Winter 2026

Here's our latest Aquatic Quarterly Update. This update includes recent project highlights, examples of how ARI's Aquatic Ecology staff influence change, as well as publications, presentations and engagement efforts. Check out each story below:

A Golden Perch otolith

Native fish populations in the Murray–Darling Basin have declined because of river regulation, habitat degradation and barriers to fish movement. Management actions such as environmental water delivery and fish stocking aim to support recovery, but it is often difficult to determine whether population changes are driven by natural recruitment, stocking or fish moving between waterways. Understanding these drivers is essential for evaluating management outcomes.

To address this issue, ARI analysed otolith (ear bone) chemistry and age data from more than 700 Murray Cod and Golden Perch collected across 13 northern Victorian waterways. Otoliths record water chemistry throughout a fish’s life, which allows us to identify where fish were born and track their movement patterns. Fish from both stocked and unstocked systems were analysed to determine the relative contribution of natural recruitment, stocking and migration.

Results showed that natural recruitment remains an important contributor to both species, although its importance varies among waterways. For Murray Cod, natural recruitment dominated populations in rivers such as the Goulburn and Broken, despite ongoing stocking, while other systems showed mixed recruitment sources or greater reliance on stocked fish. The Mitta Mitta River remained largely dependent on stocking.

For Golden Perch, approximately 62% of fish were naturally produced and 38% were hatchery-origin. Most naturally recruited fish originated from the Murray River, followed by the lower Darling River and the Goulburn–Broken system. The study also demonstrated strong connectivity between waterways, with fish produced in one river contributing to populations elsewhere.

These findings highlight that both natural recruitment and connectivity are critical to sustaining fish populations. In many Victorian tributaries, maintaining connections with the Murray River and supporting fish movement may be more important than promoting local spawning alone. The results will help managers better target environmental water delivery, evaluate outcomes and focus stocking where it is most needed. For further information see: Tonkin et al. (2026) 

Measuring a mussel

Freshwater mussels are important components of freshwater ecosystems and provide a range of ecosystem services including nutrient cycling and water purification from filter feeding of the water column. Unfortunately, their populations have suffered from global declines, but little is known about their current status in the Mallee region of Victoria. ARI surveyed six wetlands in the Hattah Lakes system and two in Merbein Common (including Brickworks Billabong) to understand where mussels occur and how populations are faring. Some of these sites are particularly important to Traditional Owners, with large shell middens still apparent.

The study used a combination of methods - including visual shoreline surveys, tactile (brail) searches in the sediment, and side‑scan sonar - to improve the chances of detecting mussels in different conditions and habitats. This combined approach provides a more reliable picture of populations than any single method alone.

Very few mussels were found, with only one live individual detected and mostly old shells remaining, indicating a major decline from historically abundant populations. These findings are significant because freshwater mussels are both ecologically and culturally important in the region. The baseline data generated here provide an important first step toward developing the research and monitoring programs needed to better understand mussel ecology in the region and work toward the recovery of healthy populations.

This project has strong support from Traditional Owners and the Mallee Catchment Management Authority (MCMA). Water managers, government agencies and Traditional Owner groups can use this information to guide future monitoring and recovery actions. This work was funded by the MCMA.

A barrier that protects Barred Galaxias

ARI scientists have spent decades researching and monitoring the endangered Barred Galaxias. This small native fish is now restricted to a few headwater streams in Victoria’s Goulburn catchment, above instream barriers. Our work has helped identify key threats and guide conservation actions, including the protection and monitoring of barriers that prevent invasive trout from reaching remaining populations. Barriers - both natural and constructed -play a crucial role by preventing trout from moving upstream where they can prey on Barred Galaxias.

ARI scientists recently teamed up with Taungurung Land and Waters Council (BIIK) staff to check the Barred Galaxias populations, 4–6 years after their last survey. The team surveyed six sites, assessing fish numbers, recruitment, barrier condition, and whether trout were present above barriers.

The results were encouraging; populations are persisting, with good numbers and evidence of recent breeding. All barriers were functioning well, with no trout detected upstream. A purpose-built barrier installed to replace an ageing log jam is also performing strongly, continuing to protect this threatened species .

This work was funded by the Goulburn-Broken Catchment Management Authority. ARI has a long history of research and monitoring of galaxiid species, including Barred Galaxias.

Azure Kingfisher (photo: Nevil Amos)

Waterbird monitoring and environmental watering in the Murray-Darling Basin have traditionally focused on wetlands and floodplains, reflecting their recognised importance for supporting large waterbird populations and breeding events. However, most of the environmental water delivered in systems such as the Goulburn is managed as in-channel river flows, and there has been limited investigation of how these flows influence waterbird habitat and resources. As a result, the extent to which river flows benefit waterbirds has remained poorly understood. ARI reviewed existing information to understand how waterbirds use rivers, including scientific publications, bird observation (citizen science) data, game duck surveys, and bird tracking studies.

This review found that:

What this means for management:

These findings can help inform the management of environmental water to maximise its benefits. Environmental flows can be designed to support waterbirds by:

This work shows that rivers can be managed to deliver multiple ecological benefits, supporting waterbirds alongside fish and vegetation. It was funded by the Flow‑MER (Monitoring, Evaluation and Research) Program, which aims to understand how rivers, wetlands and floodplains respond to Commonwealth environmental water and to improve future water management. See DCCEEW (2026) (p171-). ARI’s role in Flow-MER is outlined here. 

A fish trap within a keyhole fishway

Many barriers, including dams, weirs and barrages, have been built across Victoria’s waterways, restricting fish movement and reducing the abundance and diversity of native fish populations.

Over the past 40 years fishways have been installed to restore connectivity. However, many older structures, which were some of the highest priorities for fish passage, require maintenance, remediation or performance assessment. Fishway design has improved and evolved significantly over time. Some fishways have not been adequately monitored to confirm they are effectively passing Victorian fish species under a range of flow conditions. As climate change affects river systems, ensuring fishways are functioning as intended will become increasingly important. Substantial investment in river rehabilitation actions such as environmental flows to benefit fish also rely on their ability to successfully move through rivers.

The Victorian Fishway Functionality Assessment Project first identified and prioritised fishways needing assessment, with several high-priority sites located in northern Victoria. Three priority fishways in the Murray-Darling Basin (Kennedys Weir and Sheirs Weir on Broken Creek and the Little Murray River Weir fishway) are being assessed to determine if they are operating as designed and passing target fish species and size classes.

The findings will help guide fishway management, future infrastructure investment and environmental water delivery. By ensuring fishways are working effectively, managers can improve fish movement and maximise ecological outcomes from existing investments - delivering more benefits for native fish from every dollar spent and every drop of environmental water delivered. This work is funded by DEECA Water and Catchments.

Red Water-milfoil in Outlet Creek

ARI monitors wetland vegetation across Victoria to support environmental water planning, delivery, reporting, and long-term data collection. Over the past year, ARI surveyed 32 wetlands in the Corangamite, Goulburn Broken, Mallee, North Central, West Gippsland and Wimmera regions. Wetlands are prioritised by CMAs to update Environmental Water Management Plans, address gaps in vegetation data, and track how plants respond to recent environmental watering.

Notable findings include:

*national classifications (Environment Protection and Biodiversity Conservation Act 1999), Victorian classifications (Flora and Fauna Guarantee Act 1988)

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