Trace elements (TEs) play a key role in many biogeochemical processes, but the pathways through which TEs are input to the forest soil are still not fully understood. This study evaluates the dynamics of TEs input through atmospheric deposition and litterfall at different elevations, under different canopy coverage, and in different months in Qinghai spruce and Qilian juniper forests of the Qilian Mountains, China. We estimate the mean residence time (MRT) of TEs in organic horizons and predict the increments of TEs concentrations in forest soil. Our results indicate that the fluxes of Zn in atmospheric deposition (5.14-10.5 mg m- 2 a-1) and litterfall (4.92-19.0 mg m- 2 a-1) were the highest. The lowest fluxes of Hg and Cd were 3.03-574 and 16.3-106 mu g m- 2 a-1 in atmospheric deposition and 18.0-56.5 and 3.42-20.4 mu g m- 2 a-1 in litterfall, respectively. Atmospheric deposition input more Cd, Pb, Hg, and As into forest soils than litterfall did. The MRT of Cu, Cd, Pb, Ni, Cr, Hg, and As in the Qinghai spruce forest were 157, 148, 211, 247, 319, 73, and 195 a, which were 1.5, 5.5, 1.8, 2.0, 1.9, 36.5, and 1.4 times longer than those in the Qilian juniper forest, respectively. The concentrations of TEs in the soils will increase rapidly in the next 30 years. Our study highlights the role that TEs input through atmospheric deposition and litterfall can trigger the long-term accumulation and retention of TEs in forest soil, which may pose ecological risks.