While North America and Europe have been recovering from acidification, China is experiencing impacts of acid deposition. The Taihu region is a seriously impacted area by acid rain in China, with the average rainfall pH < 5. However, the acid neutralizing capacity (ANC) and pH of Taihu Lake have significantly increased over the past 60 years (p < 0.05). Analyses showed that watershed neutralization by carbonates and in-lake alkalinization by algae activities were the two major reactions responsible for the increase. In the Taihu basin, the dominant carbonate bedrocks are the major source of base cations (particularly Ca2+ and Mg2+) and act as the acidification buffer. In addition, our field measurements across the lake showed that the pH values were significantly higher in algal bloom waters than in areas without blooms. This observation was further supported by our statistical analysis showing that the Taihu ANC and pH were significantly correlated with the chlorophyll increase (p < 0.05; 1985-2015). However, our regression analysis indicated that the base cations in the watershed would be depleted by the early 2040s if the acid deposition continues at the current rate. Our results suggest that interactions between human accelerated weathering, watershed geochemistry, and in-lake algae activities significantly impact the water chemistry of the lake. We urgently recommend an "integrated and balanced" recovery plan for the lake ecosystem.