The capability of Salmonella to survive outside a host is especially relevant in tropical regions, where the environmental conditions could be more suitable for its long-term persistence. This study investigated the prevalence and genetic diversity of salmonellae within rivers of the Culiacan Valley in the northwestern region of Mexico. From July 2008 to June 2009, a total of 138 water samples were evaluated for the presence of Salmonella spp.; additionally, its association with environmental parameters was determined using Generalized Additive Models (GAMs). Salmonella spp. were isolated from 111 (80.4%) samples without any statistical influence on the environmental parameters investigated, according to the GAM analysis. Twenty-four serotypes were identified; the most frequently isolated serotypes were Salmonella Oranienburg (25%), Salmonella Saintpaul (9%) and Salmonella Minnesota (6%). Diverse genetic variants of Salmonella Oranienburg were found distributed across the valley with no distinctive geographical or temporal patterns. The high persistence of Salmonella spp. and the lack of differentiation of types found along the river basins suggest the existence of non-point source contamination. Furthermore, the discrepancy between the prevailing serotypes in human infections and those identified in this study denotes a limited influence of these aquatic environments in bacterial dissemination and disease transmission.