This study aimed to quantify the effect of base cation exchange (BCE) in the buffering of nitric acid produced by soil nitrification and evaluate the impact of this process on karst carbon sinks. We collected limestone soils from subtropical karst regions in southern China and established five pot simulation experiments with different fertiliser gradients. The results follow: (1) Soil calcium carbonate (CaCO3) and alkaline cations decreased gradually with increasing nitrogen application. Furthermore, the concentrations of soil leachate nitrate (NO3–N), calcium (Ca), and magnesium (Mg) gradually increased and varied within the ranges of 0.15–15.33, 28.10–85.76, and 6.53–34.35 mg L−1, respectively. (2) Soil buffering against nitrification-generated acid could be accomplished fully in the top 10 cm of the soil. At a fertiliser application rate of 100 kg N ha−1a−1, nitrification acid production was fully buffered by BCE, and soil CaCO3 was dissolved entirely by soil CO2. When the fertiliser application rate increased from 250 to 700 kg N ha−1a−1, BCE buffered approximately 55% of the H+. Soil carbonate buffering was approximately 45%. (3) Losses of Ca and Mg from the soil were induced by three processes: carbonic acid dissolving soil CaCO3, BCE and nitric acid dissolving soil CaCO3. Previous studies have ignored the contribution of BCE to groundwater Ca and Mg, leading to an overestimation of approximately 55% in the previously calculated proportion of nitric acid involved in the dissolution of carbonates.