The regional element budgets are primarily important to understand the function of ecosystems and to establish the corresponding management practices. This study takes three adjacent small watersheds (F:100% forest, FA1: 82% forest + 18% farmland and FA2: 76% forest + 24% farmland) with different land uses as the monitoring areas, which are located in the granitic region of subtropical China. Element inputs in rain water and outputs in stream water were detected and quantified from March of 2007 to February of 2010. The characteristics of element budgets at watershed scale and their effects on soil acidification were discussed. The results showed that the total ion input in the rain water was 181.74 kg/(hm²·a), with the summer input accounting for 45%. Ca²⁺, Na⁺ and NH₄⁺ contributed 80%to the total Cation input while SO₄^2- and NO₃^- contributed 74% to the total anion input, respectively. The total ion outputs in stream water of the three watersheds (F, FA1 and FA2) were respectively 236.81, 153.17 and 243.36 kg/(hm²·a), with summer output accounting for 39%-47%. Ca²⁺ and Na⁺ contributed 81%-86%, to the total cation output while SO₄^2- and NO₃^- contributed 65%-70% to the total anion output. The element budgets of the three watersheds (F, FA1 and FA2) based on precipitation input and stream output demonstrated that there was a net sink of SO₄^2-, NO₃^-, Cl^-, H⁺and NH₄⁺, while a net source of Ca²⁺, Mg²⁺ and Na⁺. SO₄^2- showed the highest net retention, while Na⁺ showed the highest net export. The net retention of SO42– in the three watersheds (F, FA1 and FA2) were 13.7, 30.43 and 20.49 kg/(hm²·a), respectively, while the net exports of Na⁺in the three watersheds (F, FA1 and FA2) were 28.99, 14.96 and 31.76 kg/(hm²·a), respectively. H⁺ input directly from acid rain was 818 mol/(hm²·a), while H⁺ production from nitrogen transformation in the three watersheds were 396, 389 and 401 mol/(hm²·a), accounting for 32%-33% of the total H⁺ input, respectively. Soil acidification rates in the three watersheds (F, FA1 and FA2) were 996, 1 069 and 1 035 mol/(hm²·a), respectively, showing that the rates of soil acidification in watersheds (FA1 and FA2) with agricultural activities were higher than that of forest watershed (F), even though the element inputs from agricultural fertilization was not taken into account.