Abstract Soil acidification rate is an essential parameter to assess the vulnerability and sustainability of various ecosystems to acid deposition. The acid-buffering mechanism of soil system includes two major proton (H+) consumption pathways, i.e., mineral weathering and cation exchange in which the former consumes directly H+ and does not lead to soil acidification while the latter would cause soil acidification by exporting base cations. However, no available method distinguishes between H+ consumed by the two pathways, so soil acidification may have been overestimated as the bulk H+ consumption. Here we establish a method to differentiate the two major H+ consumption pathways quantitatively using the stoichiometric relations between silicon (Si) and base cations of rock, soil and stream water in a typical undisturbed forested watershed in subtropical China. The results showed that a large quantity of external H+ was stored in soil from acid deposition, and the H+ concentration in soil was further affected by the transformations and specific adsorptions of extraneous nitrogen (N) and sulfur (S) compounds. The net input of H+ into the soil resulting from both wet and dry deposition was about 1395 mol ha− 1 yr− 1. The base cations from weathering was about 46% of the total net output of cations as calculated using the net output of Si by stream and the release ratio of base cations over Si during the weathering reaction of plagioclase, the predominant weatherable mineral in the area. The remaining output of base cations was attributed to cation exchange. Based on the ratio of H+ consumption by weathering and cation exchange, the actual soil acidification caused by cation exchange was estimated as 703 mol ha− 1 yr− 1, only about half of the net input of protons, which was substantially lower than the previous results obtained with no distinction between H+ consuming pathways. However, even taking the contribution of mineral weathering into account, the high net output of base cations indicates that the already acidic soil system is still depleting its base pools. This study provides a solution to estimate actual soil capacity to resist acid attack, which is crucial for reliable assessment of ecosystem resilience against external acid input.