Soil acidification along with base cations loss degrades soil quality and is a major environmental problem, especially in agroecosystems with extensive nitrogen (N) fertilization. So far, the rates of proton (H+) production and real soil acidification (loss of base cations) remain unclear in subtropical agricultural watersheds. To assess the current status and future risk of soil acidification in subtropical red soil region of China, a two-year monitoring was conducted in a typical agricultural watershed with upland, paddy fields, and orchards where high N fertilizers are applied (320 kg N ha−1 yr−1). H+ production, neutralization and base cations losses were quantified based on the inputs (rainwater, inflow of water, and fertilizer) and outputs (outflow of water, groundwater drainage, and plant uptake) of major elements (K+, Ca2+, Na+, Mg2+, Al3+, NH4+, NO3−, SO42−, Cl−, and H+). The result showed that total H+ production in the watershed was 5152 molc ha−1 yr−1. N transformation was the most important H+ source (68%), followed by excess plant uptake of cations (25%) and H+ deposition (7%). Base cations exchange and weathering of minerals (3842 molc ha−1 yr−1) dominated H+ neutralization, followed by SO42− adsorption (1081 molc ha−1 yr−1), while H+ and Al3+ leaching amounted to 431 molc ha−1 yr−1, only. These results state clearly that despite significant soil acidification, the acidification of surface waters is minor, implying that soils have buffered substantially the net H+ addition. As a result of soil buffering, there was abundant loss of base cations, whose rate is significantly higher than the previously reported weathering rate of minerals in red soils (3842 vs 230–1080 molc ha−1 yr−1). This suggests that the pool of exchangeable base cations is being depleted in the watershed, increasing the vulnerability of the watershed, and posing a serious threat to future recovery of soils from acidification.