Cultivation of a species or population and distribution to various regions has raised the idea of negative impacts on native species. The effect of non-native species on native species may be caused by competition for source, predation, hybridization, and parasite/disease transport. The present study aims to evaluate the possible effects of a trout farm established on the banks of Kocabas Stream (canakkale, Turkey) on feeding characteristics of some freshwater fish (Phoxinus phoxinus, Barbus oligolepis, and Squalius cii). The samples were collected monthly over a year at two stations located before and after the trout farm and at a control station on the tributary not impacted by the effects of the farm. Fish and environmental samples were gathered monthly with an electroshocker and some fishing tools between August 2015 and July 2016. The fish diet and resource incorporation into biomass were evaluated by gut content and stable isotope analyses. Changes in diet preferences when the species are exposed to source stresses and some individuals fed on farm-based feed contaminated from the farm in Kocabas Stream. In this study, it was observed that native fish populations in aquaculture regions were influenced by diet preferences. Designing enclosed systems limiting feed and waste transit in aquaculture establishments may be suitable for sustainability of these species.