The objective of this study was to determine the seasonal and downstream water quality variations of the San Pedro River in Chihuahua, Mexico. Water samples were collected monthly from October 2005 to August 2006 in triplicate, totaling 165 water samples. The five sampling locations were: below the Francisco I. Madero dam (LP); between Rosales and Delicias (RD); Meoqui (M); El Torreon (ET), and Julimes (LJ). The levels of As, Be, Ca, Cd, Co, Cu, Cr, Fe, Li, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sr, Ti, Ta, V and Zn were measured using an Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) Perkin Elmer 2100. In addition, temperature, pH, electrical conductivity and total and fecal coliformes were determined. The statistical analysis considered a factorial treatment design; where factor A was the location point and factor B was sampling date. In addition, a multivariate technique looking for principal components was performed. The results indicated that some samples exceeded Mexican standards for As, Be, Ca, Cd, Co, Cr, Fe, Mn, Ni, Pb, Sb, Se, Sr and Zn. The As level must be considered for a red flag to the communities along the Rio San Pedro because both the monthly average level (0.10 mg L−1) and location (0.10 mg L−1) exceeded the Mexican and International norms. The multivariate analysis showed a predominant aggregation at the LP location, meaning that there was a predominance of As, Sr, Fe and Li. At the rest of the locations the elements did not present a tendency for aggregation. Statistics applied to sampling month showed that December, January, March and April were aggregated in a negative quadrant of component 1 indicating a predominance of V, Ni, Be, Fe and As. Overall, the results confirmed that this stretch of the San Pedro River is contaminated with heavy metals and other contaminants that might affect human health as well as the health of the ecosystem.