<p>This study conducted a three-year field monitoring program from 2022 to 2024 in a 62.68 km² agricultural area in northern Guangdong, China. We systematically investigated the environmental behavior and accumulation characteristics of eight heavy metals (Cd, Hg, As, Pb, Cr, Cu, Zn, and Ni) in lightly contaminated farmland soils. Soil heavy metal concentrations showed no significant inter-annual differences over the three years (<i>P</i> &gt; 0.05). But clear spatial enrichment patterns were observed. Among four input pathways and three output pathways, atmospheric deposition was the main input source for Cd, Pb, Cr, and Zn. It contributed 63.09% to 89.19% of total inputs. Crop harvest was the main output pathway for most heavy metals. Input and output fluxes varied significantly among years for different heavy metals, especially for surface runoff and leaching water, which had significant effects on all metals except As (<i>P</i> &lt; 0.05). The theoretical changes in soil heavy metal concentrations, calculated based on net fluxes, showed weak correlations with the actual monitored values (<i>R</i>² &lt; 0.25), which might be attributed to the buffering capacity of the soil. This study provided critical field-based data to support the precise management and risk mitigation of heavy metals in lightly contaminated agricultural soils.</p>