Agricultural soils were collected from Mocorito river basin, to determine potentially toxic elements (PTEs) subtotal concentrations and geochemical fractionation, and evaluate their environmental and health risks. All sites showed low As and Cr concentrations. Subtotal concentrations (mg/kg) ranged between 6.8 and 25.6 for As, 1.9 and 2.5 for Cd and 22.5 and 55.1 for Cr. These values were classified as moderately contaminated for As, while a considerable contamination was presented for Cd and Cr. Geochemical partitioning revealed that PTEs are strongly linked with residual phase. Arsenic was associated with amorphous Fe-oxyhydroxides. Ecotoxicological indices showed from low (As and Cr) to considerable (Cd) potential ecological risk factors; potential non-carcinogenic risks by As, Cd and Cr, and potential carcinogenic risks by As and Cr. Lithogenic and anthropogenic sources were identified. Arsenic and Cr showed lithogenic influence, while Cd increased, caused by nearby activities, representing an environmental and health risk.