The Enlarged Cotter Dam (ECD) poses several threats to the only viable population of endangered Macquarie perch (Macquaria australasica) in the ACT. This study is investigating changes in food resources for Macquarie perch and rainbow trout in the early filling stage of the ECD. During the early filling stage trophic upsurge is likely to occur, following flooding and the resulting breakdown of terrestrial vegetation, leaf litter and organic matter in top soils of the reservoirs inundation zone. This is expected to result in a change in fish food resources through an increase in the production of invertebrates, the predominant dietary items of Macquarie perch. Macquarie perch and rainbow trout diet and fish food resources were sampled in the ECD before reservoir filling and in the early stages of filling, with trout diet and food resources also collected from two other existing reservoirs in the Cotter System. Preliminary results show that there are differences between the diets of fish across the three reservoirs. Food availability results also show there are significant differences in food resources across different habitats and between the three reservoirs, with complex habitats being more productive. It is important to understand the impact enlargement of reservoirs has on fish diet changes and fish food resources, as changes in food availability may affect fish condition, and potentially reproductive output. Knowledge gained from this project will be used to enhance future management decisions surrounding reservoir filling and the implications for native freshwater fish species.