The use of fish communities to evaluate stream habitat typically requires that the community at a target site be compared with concurrently or recently sampled reference communities at nearby sites. For this approach to be effective, spatial and temporal variation in the reference communities of a region must both be known. This study relates 307 recent (1976–1994) fish survey records in the Schuylkill River drainage, southeastern Pennsylvania, to four concurrent measures of water chemistry (pH, conductivity, alkalinity, hardness), two measurements of stream size (stream order, stream width) and three variables describing site position within the drainage network (elevation, link number and C-link number defined herein). Based on canonical correspondence analysis, stream size and position within the watershed influenced fish species composition more strongly than did water chemistry. Species richness, dominated by the families Cyprinidae (minnows) and Centrarchidae (sunfishes), increased from a median of four species in 1st-order streams to 21 species in 5th-order streams. Secondly, recent frequencies of occurrence are compared to frequencies inferred from historical collections using log-linear analysis. Nine species have increased in frequency, while the frequencies of eight species have declined. Eighteen species, or about ⅓ of the recent community, have been introduced. All but three of these introduced species were absent from collections before 1931, and many are now widespread. Several previously common species associated with clear, vegetated streams are now uncommon or rare (e.g., Esox americanus americanus, Notropis bifrenatus); one species, N. chalybaeus, was not found in the recent dataset. Substantial historical changes in the fish community thus accompany the influences of stream habitat and location in determining species composition at sites within the drainage.