Food webs in north-western Australian rivers exist in dynamic environments and will be influenced by land use practices, invasion of toxic cane toads (Rhinella marina) and the effects of climate change on river flows. Baseline studies are needed to understand aquatic food webs before these impacts. In the present study, we investigated the diets of two turtles (Emydura victoriae and Chelodina burrungandjii) in four upland rivers across a gradient of rainfall and land uses in the Kimberley Plateau of Western Australia. We captured turtles by snorkelling and recovered their prey by stomach lavage. We enumerated 2720 prey items from 390 E. victoriae samples and 308 prey items from 155 C. burrungandjii samples. Prey compositions distinguished E. victoriae as an omnivorous generalist relying on a diversity of animal and plant prey and C. burrungandjii as a piscivorous specialist, but with both species as likely predators of toxic cane toad eggs or tadpoles. Comparisons among the rivers showed variation in diets for both species that reflect differences in prey availability and location-specific food webs. Terrestrially based food sources were observed in 26% of E. victoriae samples and 3% of C. burrungandjii samples, which indicates the importance of the aquatic-terrestrial interface and land use practices within these rivers.