Thinning intensity is an important factor affecting water quality within a forest ecosystem. However, there has been little research on the effects of forest thinning on water quality. This study investigated the relationship between forest thinning and rainwater chemistry to quantify the effects of thinning intensity on forest water quality. Five experimental field plots with different thinning intensities (0%, 5%, 10%, 15%, and 20%) were established in a natural prunus armandii forest of the Huoditang in Qinling Mountains. Rainwater samples were collected twice a month from June to September in 2012 and 2013. Water chemistry was measured to analyze the chemical effects of tending and thinning intensity on throughfall and litterthrough. Our results showed that thinning intensity had strong relationships with forest water chemistry. Rainwater was slightly acidic, and both the forest canopy and litter layer could reduce the pH value of rainwater, which decreased with increasing thinning intensity. The pH value was 0.48 in throughfall and 0.65 in litterthrough, which was highest in the plot with a thinning intensity of 5%. The concentrations of SO₄^2-, NO₃^-, and PO₄^3- increased as they passed through the forest ecosystem. Both the canopy and litter layers showed strong SO₄^2- purification in the plot with 20% thinning intensity. The increases of SO₄^2- concentration were statistically significant when compared with NO₃^- and PO₄^3- concentrations in the control plots, with fewer significant relationships in the plots with higher thinning intensities. The increase of SO₄^2- concentration was 4.422 mg/L in throughfall and 1.5 mg/L in litterthrough, compared to the concentration in the thinning plots. A sharp decline in NO₃^-, NH⁺₄, and PO₄^3- concentrations was observed in the 5% thinning plots, compared to concentrations within the control plot, with decreases of 56.3%, 46%, and 9.2% in throughfall and 64.6%, 45%, and 60.8% in litterthrough, respectively. The capability for K ⁺, Ca²⁺, and Mg²⁺ leaching in the plots with a thinning intensity of 10% was significantly greater than the leaching capability in the other plots. The increasing fractions of Ca²⁺ and Mg²⁺ were as high as 89.9% and 120%, respectively, in throughfall, whereas the rising fractions were only 72.4% and 40%, respectively in litterthrough. The increase of K⁺ was not significant. The rainwater in throughfall and litterthrough contained little Pb²⁺, Zn²⁺, and Cd²⁺ because of the interceptions of different forest layers. The thinning intensity was also strongly related to the changing tendency of heavy metal ions. Compared with the control field plot, the concentrations of Pb²⁺, Zn²⁺, and Cd²⁺ were lower than those in the thinning plots. The plots with 20% thinning intensity showed the highest capability for intercepting and aborting heavy metals. The concentrations of Pb²⁺, Zn²⁺, and Cd²⁺ reduced by 10.6%, 22.4%, and 33.5%, respectively. Therefore, the canopy and litter layer in the plot with 20% thinning intensity had the strongest ability to intercept Pb²⁺, Zn²⁺, and Cd²⁺ from rainwater.