Freshwater turtles are threatened globally; however, short-necked turtles in Eastern Australia have been particularly successful in exploiting natural and man-made permanent water bodies. The catchments of eastern Australia offer a unique opportunity to compare the diets of species in habitats where both genera coexist, but only one genus is usually locally dominant. We compared the diets of species of Emydura and Myuchelys and Flaviemys in inland and coastal catchments in eastern Australia to determine the breadth of diets. We also conducted a more in depth study of the ecology and habitat preferences of the Bellinger River Emydura (Emydura macquarii macquarii) and Myuchelys georgesi. We found that diets of short-necked turtles on the east coast of Australia are separated by water conditions, and largely independent of species and location. Species of Myuchelys and Emydura are omnivorous. A high proportion of their food is from benthic macro-invertebrate communities in clear water. Terrestrial invertebrates and filamentous algae are present more in the diets of species inhabiting turbid water. Competition between species of Emydura and Myuchelys/Flaviemys is likely to occur when in sympatry, because species of Emydura can adapt their diets to various habitats and water quality. Myuchelys georgesi is restricted to, but common in, the Bellinger River. Interspecific competition may occur between E. m. macquarii and M. georgesi because of similar habitat preferences, diets and life histories. Emydura m. macquarii is not unique to the Bellinger River and hybridization with the endemic M. georgesi is a threatening process.