To explore long-term trends of acid anions in the rain water in Lake Taihu watershed, the lake water and their environmental implications, the variation characteristics, sources and the relationships of SO₄^2-, NO₃^- in the rain water and the lake water were studied via historical data collection and sampling analysis. The results indicated that SO₄^2- in the rainwater showed a significant decreasing trend since 1990s with an annual average decrease rate of 0.28 mg/(L·a), and the NO₃^- showed a significant increasing trend with an annual average increase rate of 0.05 mg/(L·a), which suggests an aggravating trend of nitrogen pollution in the rain water. In contrast, SO₄^2- in the lake water showed a significant increasing trend with an annual average increase rate of 1.24 mg/(L·a), and the NO₃^- showed a significant decreasing trend with an annual average decrease rate of 0.02 mg/(L·a). During the past 30 years, the ratio of SO₄^2-/NO₃^- in Lake Taihu water continuously increased, much higher than that of the rain water. The research indicated that the acid deposition caused by SO₂ emissions in the watershed was mainly responsible for the increased concentration of SO₄^2- in the lake water. However, the nitrogen oxides emissions did not cause an increase concentration of NO₃^- in the lake water, indicating that Lake Taihu watershed plays a significant role in the retention of nitrogen deposition, while the lake water is an important sink for sulfate deposition. The regional nitrogen deposition has an important impact on Lake Taihu water eutrophication. It is of great significance to prevent the acidification and eutrophication in Lake Taihu via comprehensive management of acid emissions in Lake Taihu watershed.