Consumers usually respond to variations in prey availability by altering their foraging strategies. Generalist consumers forage on a diversity of resources and have greater potential to ‘switch’ their diet in response to fluctuations in prey availability, in comparison to specialist consumers. We aimed to determine how the diets of two specialist species (the eastern long-necked turtle (Chelodina longicollis) and the broad-shelled turtle (Chelodina expansa) and the more generalist Murray River short-necked turtle (Emydura macquarii) respond to variation in habitat and prey availability. We trapped and stomach-flushed turtles, and compared their diets along with environmental variables (turbidity, macrophyte and filamentous green algae cover, and aquatic invertebrate diversity and abundance) at four wetlands in north-central Victoria. Diets of E. macquarii differed from those of both Chelodina species, which overlapped, across all four sites. However, samples sizes for the two Chelodina species were too small to compare among-wetland variation in diet. Dietary composition of E. macquarii was variable but did not differ statistically among sites. Emydura macquarii preferentially selected filamentous green algae at three of the four sites. Where filamentous green algae were rare, total food bolus volume was reduced and E. macquarii only partially replaced it with other food items, including other vegetation, wood, and animal prey. Many turtles at these sites also had empty stomachs. Thus, filamentous green algae may be a limiting food for E. macquarii. Although E. macquarii has previously been described as a generalist, it appears to have limited ability to replace filamentous green algae with other food items when filamentous green algae are rare.