Salmonella enterica is an important foodborne pathogen, and contamination of surface and ground water that may result from various human activities, such as animal production and urbanization, may contribute to the public health burden. The aims of this study was to determine the sources of Salmonella contamination in four different types of watersheds and to assess the relative contribution of multidrug-resistant strains. Eighty-six water samples collected from four different watershed systems, including those impacted by swine production (n = 12), residential/industrial (n = 34), crop agriculture (n = 12), and forestry (n = 28), were cultured for Salmonella and further characterized by serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis genotyping. Salmonella prevalence was high in all four watersheds: residential/industrial area (58.8%), forestry (57.1%), crop agriculture (50%), and swine production (41.7%). Majority of the Salmonella isolates (87.1%) were pansusceptible. Multidrug resistance up to eight antimicrobials (R-type: AmStTeAxChCeKmGm) was detected in water samples that originated from swine production systems only. Serovars identified included Anatum, Gaminara, and Inverness (18.3% each) and Muenchen and Newport (8.7% each), Bredeny (7.6%), and Montevideo (6.8%). Pulsed-field gel electrophoresis analysis indicated genotypic relatedness among Salmonella recovered from residential/industrial and forestry-associated watersheds (genotypic cluster types A, C, D, E, F, G, H, and J), sites with relatively close geographic proximity. Swine-production-associated isolates were distinctly different from the others (genotypic cluster types B and I), corroborating the phenotypic findings. Overall, the findings suggest that all the various watersheds, including natural forest, remain important contributors of Salmonella contamination. While swine-production-associated water samples were not found to have a disproportionately high prevalence, it was the most important reservoir of multidrug-resistant strains.