Physical cage aquaculture structure can attract native fish species in marine and freshwater ecosystems. Most studies on the effects of cage farms on native fish distribution have been undertaken in marine environments and outside of Asia as the main freshwater cage aquaculture producing region. Many studies have emphasised connections between native fish distribution and feeding time. Previous research also has shown the necessity to use modelling to monitor this effect to reduce data collection costs. Here we analyse the distribution of an endemic fish species, Rasbora maninjau, and a native fish, Gobiopterus sp., associated with tilapia cage aquaculture occurrence using a Maximum Entropy Model (MaxEnt). We find that the application of the MaxEnt model can produce reliable and accurate information on the impacts of cage aquaculture on the native fish species distribution aligning with the more expensive count data method. Our results also suggest that the species-specific interaction between the native fish and cage farms is mainly arising from an interaction between the ecological behaviour of the native fish with dimensions of the environmental condition such as turbidity. Our study therefore highlights the importance for improved appraisal of the ecology of native fish in the cage aquaculture risk assessment.