The increase in population in the Utcubamba River basin without the corresponding implementation of wastewater treatment systems by the authorities has led to a decrease in water quality, which constitutes a threat to public health and the ecosystem preservation. The objective of this work was to reduce the data collected in large hydrographic basins, both at the sampling stations level and at the level of variables. Sampling was carried out at 43 sites located in the main channel and major tributaries, and their physicochemical and microbiological quality were analyzed through the determination of 19 variables during three different seasons (early rains, rainfall and drought). Multivariate statistical methods (correlation analysis, principal component analysis and cluster analysis) were applied to find the cause of natural or anthropogenic sources of pollution and its distribution in the basin. The results show that the main parameters that spatially affect the basin are a result of high concentrations of bacteria and chemical compounds such as nitrites, phosphates and ammonium. Finally, the use of multivariate methodologies to analyze the obtained results allows to reduce the number of variables as well as sampling stations for future evaluations.