Organochlorine pesticides (OCP) and heavy metals are contaminants that threaten ecosystem health. Migratory birds can bioaccumulate these contaminants; therefore, contaminant effects should be assessed during reproductive, migratory, and wintering stages. We assessed Hg, Pb, and OCPs in the Northern Shoveler (Spatula clypeata) and Northern Pintail (Anas acuta) during their winter stay in southern Sinaloa, Mexico, evaluating associations with exposure and the effects on health-status biomarkers. These migratory ducks use a wide variety of sites in the central and western United States, Canada, and Alaska and along the Mexican portion of the eastern Pacific Flyway. Spatula clypeata showed significantly higher concentrations of Hg in feathers compared to those found in A. acuta. Although there were no differences between species in feather Pb concentrations, the concentrations were high, indicating widespread Pb contamination in wetlands along migratory routes. Compared to those of A. acuta, S. clypeata exhibited lower condition index values, higher organosomatic index values, a higher degree of Hg and OCP bioaccumulation, and a higher OCP liver/muscle ratio. Both species showed similar associations between OCP and Pb concentrations and high spleensomatic index values. Neither species exhibited a relationship between contaminants and the heterophile/lymphocyte ratio or budcells in polychromatic erythrocytes. Our results indicate that both species, despite coexisting along their migratory routes and in their wintering habitat, likely have different bioaccumulation profiles due to differences in trophic niches.