Santa Catarina State has the largest pig producers in Brazil and its West region has the highest concentration of swine production. Diagnostic assessment conducted by Embrapa Swine and Poultry Scientists in 2003 reported that more than 90% of 3,821 pig farms didn't have the required environmental license to operate. The Environmental State Promoter proposed an Adjustment Environmental Contract (AEC) to legalize these farms. Embrapa has a current project that monitors the effectiveness of AEC in terms of social, environmental and economic impacts. The aim of this research was to monitor the microbiological water quality in a subbasin of Pinhal River characterized by farmers that signed with the AEC. The subbasin is located in Concordia rural area. Eight sampling points along the Pinhal River were selected. Sampling and sample analyses occurred between the months of January and August. Total Coliform, Fecal Coliform, Escherichia coli, and Salmonella were analyzed from each sample. The sampling period of August to January was selected because it is the time of the year that many farmers prepare their soil to corn planting. The highest concentrations evaluated for the three Coliforms microorganisms were: Total Coliform, 480 UFC/ml; Fecal Coliform, 200 UFC/ml and E. coli, 280 UFC/ml. Salmonella was not present in all the samples, but in monitoring points located in the lower subbasin had higher levels of Salmonella. This microorganism could be threat to human and animal health. The AEC will continue to recommend that actions must be taken to improve the microbiological water quality of watersheds that are associated with swine production. Other results demonstrating the relationship between microbiological water quality and soil conservation, presence of riparian vegetation and use of pig waste as fertilizers will be reported.