Atmospheric wet deposition is a vital part of biogeochemical cycles in earth surface environment systems, which is not only controlled by local sources and long-range transported continental substances from natural and anthropogenic sources, but also potentially influenced by the topographical features (e.g. peak clusters and depressions in karst areas). To investigate the depression trapping effect of vertical distribution of rainwater chemical composition and evaluate the effect of trapping by depression on wet deposition flux, rainwater samples from two sites (HR, a hilltop shrubbery area, and LR, inside a depression paddy field area) of a karst agricultural depression in Southwest China, were collected during the rainy season. From these, the major ionic concentrations were measured. The results indicated a variance in pH from 4.8 to 6.4 with a volume-weighted mean (VWM) value of 5.7 at the HR, and, a range of 5.4–6.9 with a VWM of 6.0 at the LR. The VWM concentrations of ions were decreased in the order of SO4 2- > NH4 þ > Ca2þ > NO3 - > Mg2þ > Kþ > Naþ > Cl > F at both sites, and were dominated by SO4 2-, NH4 þ, Ca2þ, and NO3 - , accounting for >87% of the total ions at the two sites. The result of fractional acidity (FA) and neutralization factors (NF) revealed that the relatively high pH values were the result of neutralization of the alkaline substances (NH4 þ and Ca2þ) rather than the scarcity of acidic materials. Source analysis of major ions showed that anions were predominantly controlled by anthropogenic emission, while cations originated from both terrestrial sources and anthropogenic activity. The vertical distribution of dominant ions (NH4 þ, NO3 - , Ca2þ, Mg2þ, and SO4 2-) were ascribed to the relatively weak air convection movement within the depression area (specific atmospheric circulations) and the differences in human interference at two sites (LR, cultivated land; HR, luxuriant vegetation). This is further supported by the more negative rainwater δ15N–NO3 - values ( 8.5 to 6.0‰), in LR than that in HR ( 6.2 to 3.4‰). The depression trapping effect could significantly affect the estimation of wet deposition fluxes (up to 80.6% for Ca2þ and 68.7% for NH4 þ), which requires consideration in future studies, e.g. N wet deposi