AIM: The main objective of the study was to evaluate the limnological characteristics of rivers flowing through urban and rural areas in the upper Uruguay River basin in western Santa Catarina (SC), Brazil. METHODS: Sampling sites in the tributaries were selected along the longitudinal gradient and the different use of the soil in adjacent areas. Samples were collected bimonthly from March 2005 to August 2006. The following were analysed: depth, pH, electrical conductivity, dissolved oxygen concentration (DO), water temperature, chemical oxygen demand (COD), total alkalinity, ammonia, nitrite, nitrate and phosphorus were analysed. RESULTS: In most of the rivers analysed, we found a continuum from the spring to the river mouth that was characterised by a gradual increase in electrical conductivity, COD, phosphorus, alkalinity, nitrite and nitrate. However, an alteration from this pattern was found in rivers passing through urban areas. This deviation was due to high organic matter input poured into the rivers from these areas. CONCLUSIONS: Degraded riparian forest was observed along most of the bodies of water, which facilitates the entry of pollutants. Although the studied area suffers from intense farming activity (agriculture and livestock) and has the highest concentration of swine livestock in the country, the rivers that were most altered from their natural state were those that were influenced by sewage and industrial effluents from urban development.