Crocodilians are apex predators and sympatric species are likely to have different ecologies or morphologies in order to minimise competition between species, ie, niche partitioning. Here, we examined the ecological niche factors that may affect competition between juvenile Siamese crocodiles (Crocodylus siamensis) and Tomistoma (Tomistoma schlegelii) in Mesangat Lake—the only documented area where the two species co-exist. This location has also been subjected to recent disturbance from logging and oil palm development. We identified and compared preferred habitats and stomach contents of each species. Tomistoma schlegelii were found predominantly in flooded forests, while C. siamensis were mainly in open areas. However, overlap in prey choice between juvenile T. schlegelii and C. siamensis was significantly higher than expected by chance and invertebrates were the most frequent prey items in both species. High overlap in prey choice between the two species suggests that juvenile T. schlegelii and C. siamensis are generalist predators. Furthermore, the evidence of separation of habitat combined with overlap in prey choice indicates competition-driven niche partitioning between C. siamensis and T. schlegelii. This paper provides basis for co-ordinated conservation efforts for the two threatened species in this unique ecosystem.