The aim of this study was to examine the Salmonella serovars and antimicrobial resistance within an animal-based agriculture river system. The study area consisted of a 1,345 ha sub-basin at the upper Pinhal River catchment. Pinhal River is located in Concordia, Santa Catarina, Brazil. The sub-basin is a typical agricultural watershed. Salmonella was isolated from 241 samples (62%), resulting in 324 isolates. The most number of Salmonella sp. occurred in samples from sites associated with high stoking density animal unit per hectare area. It was possible to demonstrate the variability of serovars in the study area; 30 different serovars were found and at least 11 of them by monitoring the site. Among 180 isolates submitted to an antimicrobial susceptibility test, 50.5% were susceptible to all 21 antimicrobials tested, and 54 different profiles were found. In the current study 49.5% of the tested isolates were resistant in at least one antimicrobial, and multi-resistance occurred in 18% of isolates. Conduct studies that evaluate the detection of antimicrobial resistance in microorganisms of public interest and in surface water sources of catchments characterized by intensive animal production will assist communities, society and governments in decision-making