Elevated atmospheric deposition of strong acids contributes to short-term/seasonal acidification of surface waters draining sensitive northern forests of North America and Europe during high flow. Reducing atmospheric deposition of NO3- and/or SO42-, therefore, could improve the health of aquatic ecosystems by mitigating episodic acidification. We used an integrated biogeochemical model (PnET-BGC) to simulate the effects of acidic deposition on seasonal variations in surface water chemistry, and to evaluate emission control scenarios to decrease acidification during snowmelt. Model calculations suggest that historical long-term inputs of acidic deposition have altered the seasonal patterns in surface water chemistry. Although short-term increases in NO3- coincide with snowmelt acidification, model simulations indicate reductions in SO42- deposition result in larger benefits than an equivalent reduction in NO3- deposition. Year-around reductions in NO3- deposition are also more beneficial to the acid-base status of stream water than summer-only reductions.