To characterize the atmospheric content of chemical contaminants, samples of atmospheric deposits were collected at several sites in the mining area of the San Jorge river basin, Colombia, during La Niña events (May 2010 and October 2011). Measurements of trace metals (Hg, Cu, Cd, Pb, Ni, and Zn) were performed after rain collection using a bulk deposition sampler in locations near a point source and sampling points located within a range of 30 Km away from the mine. As expected, concentrations were elevated in locations close to the ferronickel mining area with similar levels to other highly polluted areas. Concentrations of bulk precipitation and deposition were measured for Zn (23.07 ± 7.30 ng mL−1 and 227.5 ± 22.3 μg m−2 day−1, respectively) and Ni (2.20 ± 1.35 ng mL−1 and 21.2 ± 4.79 μg m−2 day−1) close to the coal and ferronickel mining. The other metals showed higher concentrations in sites nearby the artisanal and small-scale gold mining communities; and mercury raises special concern because high values of bulk deposition were found (58.3 ± 4.4 μg m−2 day−1), suggesting an intense Hg exposure in local residents. Moreover, no patterns of temporal distribution of heavy metals deposition were found during the sampling period. Overall, these results suggest that trace metal concentrations and fluxes are comparable to other locations in the world that are impacted by regional anthropogenic sources related to mining activities.