Rivers are critical to agriculture, industry, and the needs of humans and wildlife. This study evaluates the water quality of the Beheshtabad River in Iran’s Chaharmahal and Bakhtiari Province, using water quality index and multivariate statistical methods. Nitrate, temperature, phosphate, turbidity, dissolved oxygen, biological oxygen demand, electrical conductivity, total solids, and pH were measured at five selected stations along the river over 6 months using standard methods. Water quality index results demonstrated that water quality varied in the selected stations between average and good and that pollution in this section of the Beheshtabad River increases from upstream to downstream. Clustering and principal component analysis were also utilized. Multivariate statistical methods were used to analyze water conditions for efficient management of surface water quality. Agricultural fertilizers, upstream wastewater discharge, and fish farms constitute the main elements that decrease the water quality of the Beheshtabad River. To preserve this water resource against pollution, the implementation of stringent rules and guidelines are needed to enhance health and preserve water resources for future generations.