The rapid development of the aquaculture industry in recent years and the increase in the intensity of production has raised questions regarding potential environmental impacts. Understanding intra- and interspecific relationships between native and cultured species is important for sustainable use of natural resources. This study investigated the spatial and temporal effects of a fish farm constructed next to a river on the relative abundance and diversity of natural fish populations. Sampling was conducted at three stations, upstream and down stream from a trout farm and at a control site, on Kocabas stream in Canakkale (Turkey) monthly between August 2015 and July 2016. There was no significant difference among the three stations in fish diversity. However, a remarkable seasonal and spatial variation in the composition and relative proportion of the indigenous fish assemblage were observed among the three stations. In conclusion, the fish farm might have influenced species composition and relative abundances particularly at the downstream station.