The water quality is influenced by different factors, including land use, hydrological conditions, and anthropogenic activities. The identification of the contamination sources in the Vizela river and the potential effects on water quality will promote efficient watershed management. The spatial and temporal variability of surface water was analysed through the physicochemical parameters, including: temperature, pH, Total Dissolved Solids, electrical conductivity, redox potential, and chloride, fluoride, bromide, nitrite, nitrate, sulfate, and phosphate content. The microbiological parameters Escherichia coli and intestinal enterococci were monitored over time. The obtained results show that the water located downstream the Vizela river is the most contaminated, although there has been an improvement in the water quality over time. The microbiological values are higher than the Portuguese parametric values defined for human consumption, and often also for recreational water activities. Continuous spatial and temporal water monitorization including the physicochemical and microbiological parameters is recommended as a preventive and monitoring measure.