Surface waters across much of New York State’s Adirondack Mountains were acidified in the late 20th century but began to recover following the 1990 Title IV Amendments to the Clean Air Act. Previous assessments of acidification recovery in the Adirondacks have generally been based on surface water chemistry data and inferred relationships to fish and other aquatic biota. Little data, however, has been available to characterize biological impacts and predict recovery of fish assemblages in streams of the region. Here, we use quantitative fish surveys combined with chemistry data from 48 headwater streams sampled during summer 2014–2016 to develop logistic (probability) models that characterize the status of contemporary fish assemblages and predict how different N and S deposition loads may affect future fish assemblages. Statistical models for inorganic aluminum (Al_i) and richness ≥1 species; and for acid neutralizing capacity (ANC) and total density >400 fish/0.1 ha, total biomass >1500 g/0.1 ha, brook trout Salvelinus fontinalis density >0 or >200 fish/0.1 ha, and brook trout biomass >1000 g/0.1 ha were suitable for evaluating community and population responses to changes in acid-base chemistry. Predictions of fish-assemblage responses using several of these models demonstrated that anticipated changes in national (U.S.) secondary standards for atmospheric emissions of NO_x and SO_x to achieve target N and S deposition loads are likely to alter the acid-base chemistry and the probabilities of observing various levels of brook trout population and fish-community metrics in streams across the region and elsewhere.