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The San Pedro River (SPR) is located in northern Sonora (Mexico) and southeastern Arizona (USA). SPR is a transboundary river that develops along the Sonora (Mexico) and Arizona (USA) border, and is considered the main source of water for a variety of users (human settlements, agriculture, livestock, and industry). The SPR originates in the historic Cananea mining area, which hosts some of the most important copper mineralizations in Mexico. Acid mine drainage derived from mine tailings is currently reaching a tributary of the SPR near Cananea City, resulting in the contamination of the SPR with heavy metals and sulfates in water and sediments. This study documents the accumulation and distribution of heavy metals in surface water along a segment of the SPR from 1993 to 2005. Total concentrations of Cd, Cu, Fe, Mn, Pb, and Zn in surface waters are above maximum permissible levels in sampling sites near mine tailing deposits. Nevertheless, a significant decrease in the Fe and SO₄ ²⁻ in surface water (SO₄ ²⁻: 7,180-460.39 mg/L; Fe: 1,600-9.51 mg/L) as well as a gradual decrease in the heavy and transition metal content were observed during the period from 1994 to 2005. Approximately 2.3 km downstream of the mine tailings, the heavy metal content of the water drops quickly following an increase in pH values due to the discharging of wastewater into the river. The attenuation of the heavy metal content in surface waters is related to stream sediment precipitation (accompanied by metal coprecipitation and sorption) and water dilution. Determining the heavy metal concentration led to the conclusion that the Cananea mining area and the San Pedro River are ecosystems that are impacted by the mining industry and by untreated wastewater discharges arising from the city of Cananea (Sonora, Mexico).