The accumulation of heavy metals in farmland has become an important issue related to food security and environmental risk. The annual inputs of heavy metals (As, Cd, Hg, Pb, Cr, Cu, and Zn) to agricultural soil for a full year in Hainan Island have been studied. Three fluxes through the cultivated horizon were considered: (1) atmospheric depositions, (2) fertilization, and (3) irrigation water. The corresponding samples were collected and analyzed on a large regional scale. The total input fluxes show obvious spatial variability among different regions. The inventory of heavy metal inputs to agricultural land demonstrates that agricultural soil is potentially at risk of heavy metal accumulation from irrigation water. The potential at risk of heavy metal accumulation from atmospheric deposition and fertilizer is relatively low compared to irrigation. The results indicate that Hg is the element of prior concern for agricultural soil, followed by Cd and As, and other heavy metal elements represent little threat to the environment in the study area. This work provides baseline information to develop policies to control and reduce toxic elements accumulated in agricultural soil.