Honnedaga Lake in the Adirondack region of New York has sustained a heritage brook trout population despite decades of atmospheric acid deposition. Detrimental impacts from acid deposition were observed from 1920 to 1960 with the sequential loss of acid-sensitive fishes, leaving only brook trout extant in the lake. Open-lake trap net catches of brook trout declined for two decades into the late 1970s, when brook trout were considered extirpated from the lake but persisted in tributary refuges. Amendments to the Clean Air Act in 1990 mandated reductions in sulfate and nitrogen oxide emissions. By 2000, brook trout had re-colonized the lake coincident with reductions in surface-water sulfate, nitrate, and inorganic monomeric aluminum. No changes have been observed in surface-water acid-neutralizing capacity (ANC) or calcium concentration. Observed increases in chlorophyll a and decreases in water clarity reflect an increase in phytoplankton abundance. The zooplankton community exhibits low species richness, with a scarcity of acid-sensitive Daphnia and dominance by acid-tolerant copepods. Trap net surveys indicate that relative abundance of adult brook trout population has significantly increased since the 1970s. Brook trout are absent in 65% of tributaries that are chronically acidified with ANC of <0μeq/L and toxic aluminum levels (>2μmol/L). Given the current conditions, a slow recovery of chemistry and biota is expected in Honnedaga Lake and its tributaries. We are exploring the potential to accelerate the recovery of brook trout abundance in Honnedaga Lake through lime applications to chronically and episodically acidified tributaries.