Warm water stream fish assemblages (2005) and habitat variables (2004 and 2005) were examined from May to September at 108 sites in the Tonawanda and Johnson Creek Watersheds of Western New York. Seventy species and \u3e 27,500 fishes were identified; ~98% were from Families Cyprinidae, Centrarchidae, Catostomidae and Percidae. Data were analyzed at 16 spatial scales using best subsets and backward stepwise multiple linear regression to explore associations between individual fish species ≥9% of total catch and fish assemblage variables [catch per unit effort (CPUE), species richness, Simpson’s diversity] with six habitat variables (pool type, maximum depth, substrate size, instream wood, bank cover, aquatic vegetation). CPUE was the only fish assemblage variable related to habitat variables, especially aquatic vegetation and pool type. Only two species (johnny darter, Etheostoma nigrum; round goby, Neogobius melanostomus) were significantly associated with habitat variables. The results reflected inherent difficulties understanding the complexities of habitat use by warm water stream fishes and their assemblages and how to manage them on a broad scale
