The effective conservation and management of threatened species requires comprehensive knowledge about resource utilisation. Here we integrated tissue stable isotope analysis and biotelemetry to identify the predominant dietary resources of two sympatric species of freshwater turtle, and locate where those items were acquired. We deployed an array of underwater acoustic telemetry receivers to autonomously, simultaneously, and continuously, monitor the movements of the threatened Elseya albagula and Elusor macrurus, over a 12-month period. Stable isotope (SI) values (δ13C and δ15N) were measured within the carapace of each species, and compared with SI values within potential food items. The integration of movement information and carapace SI data revealed that whilst these species had overlapping home ranges, there was less than 5% probability of inter-species dietary niche overlap. E. macrurus acquired food items consisting of bivalves, gastropods and aquatic insects within rocky riffles whilst E. albagula fed on filamentous algae and crustaceans foraged from the muddy and vegetated shallow margins of deep water pools. Our findings differ from stomach content analysis and mark-recapture studies, which reported these species to have similar habitat and resource requirements. We argue that the observed disparity is because our methods provided a weighted measure of an individual’s dietary preference and habitat utilisation over a broad time-scale, whilst stomach content analysis and mark-recapture studies offer only a single observation of an individual’s dietary preference. The research demonstrates the utility of integrating passive acoustic telemetry and carapace stable isotope analysis for identifying critical habitat for freshwater turtles.