As part of the Episodic Response Project (ERP), we studied the effects of episodic acidification on fish in 13 small streams in the northeastern United States: four streams in the Adirondack region of New York, four streams in the Catskills, New York, and five streams in the northern Appalachian Plateau, Pennsylvania. In situ bioassays with brook trout (Salvelinus fontinalis) and a forage fish species (blacknose dace (Rhinichthys atratulus), mottled sculpin (Cottus bairdi), or slimy sculpin (Cottus cognatus), depending on the region) measured direct toxicity. Movements of individual brook trout, in relation to stream chemistry, were monitored using radiotelemetry. Electrofishing surveys assessed fish community status and the density and biomass of brook trout in each stream. During low flow, all streams except one had chemical conditions considered suitable for the survival and reproduction of most fish species (median pH 6.0-7.2 during low flow; inorganic Al < 60 μg/L). ERP streams with suitable conditions during low flow, but moderate-to-severe episodic acidification during high flow, had higher fish mortality in bioassays, net down-stream movement of brook trout during events, and lower brook trout density and biomass compared to nonacidic streams, and lacked acid-sensitive fish species (blacknose dace and sculpin). Movement of trout into refugia (areas with higher pH and lower Al) during episodes partially mitigated the adverse effects of episodes. Recolonization from alkaline tributaries or microhabitats can maintain low densities of fish in streams that experience severe acidic episodes, but it is not sufficient to sustain fish densities and community composition at levels expected in the absence of these episodes. Fish responses to acid-base chemistry were fairly consistent across regions. In general, trout abundance was reduced and acid-sensitive fish species were absent from ERP streams with median pH < 5.0-5.2 during high flow and inorganic Al > 100-200 μg/L. We conclude that episodic acidification can have long-term effects on fish communities in small streams.