The aim of present study is to investigate the impacts of environmental variables to distribution and habitat preference of the species in an endorheic stream. For this purpose, the study was conducted in the Istranca Stream, which is draining into the Lake Durusu in Istanbul city, from March 2012 to June 2013, monthly. The sampling surveys were carried out at six stations on the stream, and fish samples were collected from the stations by electro-fishing. Water samples for water quality (NO2-N, NO3-N, SiO2, PO4-P, TP, Fe, SO4 ) and chlorophyll a analyses were taken simultaneously with fish sampling from the stations. At each sampling station, pH, dissolved oxygen (DO), conductivity (EC) and water temperature were measured in situ with a portable digital multiparametric analyzer. Water depth, stream width, flow rate and weather temperature were also recorded in situ. To assess the relationships between the biotic variables (fish assemblages and chl-a) and the environmental variables, redundancy analysis (RDA) was employed to explore possible patterns. During the study, a total of 20 taxa belonging to 4 families were captured from the Istranca Stream. Rhodeus amarus (Bloch, 1782) (24%), Squalius cephalus (Linnaeus, 1758) (16%) and Gobio bulgaricus Drensky, 1926 (13%) were determined as the most abundant fish species in the stream. RDA analysis explained 68% of the variation between biotic and environmental variables. Statistical analyses indicated that fish assemblages of the stream highly associated with the environmental variables; flow rate, conductivity and water temperature were the most influential.