Fish assemblages of small temperate streams are strongly influenced by harsh winter conditions, which are tolerated by year-round resident species and avoided by seasonal migrants. We tested effects of season and longitudinal position on total biomass, species abundances and body condition of fish in two neighboring streams (Plum Run, Brintons Run) in southeast Pennsylvania, USA. In each stream we sampled four pools in a downstream reach in close proximity to a larger (6^th order) stream and four pools in a more isolated upstream reach during fall, winter and spring. Total biomass depended strongly on pool volume, with which other habitat variables (area, maximum depth, extent of undercut bank) were also correlated. Downstream pools of Plum Run (mean volume 18.1 m³, link magnitude 5) had 21 fish species, including 6 species of Centrarchidae that largely vacated the pools in winter. The assemblage in upstream pools of Plum Run and in both upstream and downstream pools of Brintons Run (mean volumes 5.6 m³, 5.7 m³ and 4.4 m³, respectively; all link magnitude 2), consisted of 7 to 11 species. These pools were dominated by Cyprinidae, generally lacked centrarchids and showed little seasonal variation. Three year-round resident cyprinids [Semotilus atromaculatus (Creek chub), Rhinichthys atratulus (Blacknose dace) and Clinostomus funduloides (Rosyside dace)] and the winter emigrant Catastomus commersonii (White sucker) were the most abundant species in the two streams. Body condition of all four species declined substantially in winter; effects of longitudinal position (upstream vs. downstream) on body condition were less pronounced and varied among species. Abundances of the three resident cyprinids were all negatively correlated with the abundances of large, potentially predatory, centrarchids. Occupation of downstream pools in the larger stream by the centrarchids during fall and spring, but emigration from the study area during winter, further modified the effects of winter on the fish assemblage.