Patterns of epilithic diatom species distribution in relation to environmental variables from 12 sampling sites on the main stream and some of its tributaries in the Nilufer Stream Basin were determined using multivariate statistical techniques. The stream basin has been heavily influenced by anthropogenic effects. The upper part of the basin that is distant from pollution sources mostly has a spring water quality, while the lower part where the stream flows through the urban area and receives domestic and industrial wastewater has a quite low quality. Ordination techniques using both diatom taxa and 21 environmental variables revealed non-to slightly polluted upper basin sites and highly polluted lower basin sites along the stream. The results showed that the stream catchment is polluted gradually from upstream to downstream and that most of the downstream sites have very low water quality especially in summer months. A total of 134 epilithic diatom taxa belonging to 50 genera were recorded for 12 sample sites. Partial CCA results indicated that water temperature (T), discharge (Q), and total phosphorus (TP) were the most important variables affecting the distribution of diatom species. Unpolluted or slightly polluted upper basin sites were dominated by Achnanthidium minutissimum, Cocconeis placentula var. euglypta, Gomphonema olivaceum, and Navicula tripunctata. Highly polluted lower basin sites were characterized by high levels of organic and inorganic matters and low dissolved oxygen (DO) values. Species widespread in the highly polluted lower basin sites such as Nitzschia umbonata, Nitzschia amphibia, Nitzschia capitellata, Nitzschia palea, Nitzschia paleacea, Luticola mutica, and Stephanodiscus niagarae were mostly related to pollution indicator variables such as ammonium nitrogen (NH4(+)-N), sodium (Na+), total phosphorus (TP), and total organic matter (TOM).