Monitoring of distribution and fractionation of mercury (Hg) from within the San Juan River Basin that provides water for the Metropolitan Area of Monterrey, Mexico (MAM), was performed. The purpose of this work was to characterize the risk of Hg exposure to human populations that reside in communities nearby the area. Total Hg was quantified from water and surface sediments (0-10 cm) collected from 11 locations during the summer season of 2006. The analysis of Hg was carried out by Cold Vapor Atomic Absorption Spectroscopy (CVAAS). Simultaneously, some relevant physical and chemical parameters were analyzed in water samples and correlated to Hg concentrations to trace the fate of Hg in the watershed. In the river water samples, Hg levels were in the range from 0.17 to 1.14 |ig/L. The mean concentration level of Hg in sediment samples was 0.405±0.074 mg/Kg and showed a uniform Hg distribution along the San Juan River Basin, conversely, the fractionation studies showed that chemical speciation plays an important role in stability and low mobility.