Industrial, agricultural, and urban areas can be sources of pollution and a cause of habitat fragmentation. The Conlara River located in the northeast of San Luis Province suffers different environmental pressures along its course from urban to agro-industrial areas. The present study aims to assess the water quality of the Conlara basin by evaluating how metals and pesticide contamination as well as physicochemical parameters relate to physiological stress in Jenynsia multidentata. Samplings were carried out in four sites characterized by a growing gradient of anthropic impact from the springs to the final sections of the river, starting with tourism passing through urban areas and ending with large agricultural areas (from S1 to S4) during both the dry and wet seasons. A total of 27 parameters were determined (11 physicochemical, 9 heavy metals, and 7 pesticides) in surface waters. Biomarkers (CAT, TBARS, ChE, and MN) showed significant physiological and cytological alterations in J. multidentata depending on the hydrology season. The combination of physicochemical parameters, metals, and pesticide levels allowed typification and differentiation of the sites. Some metal (Cr, Mn, Pb, and Zn) and pesticide (α-BHC, chlorpyrifos, permethrin and cypermethrin, and endosulfan α) levels recorded exceeded the recommended Argentinian legislation values. A principal component analysis (PCA) allowed detection of differences between both seasons and across sites. Furthermore, the differences in distances showed by PCA between the sites were due to differences in the presence of physicochemical parameters, metals, and pesticides correlated with several biomarkers’ responses depending on type of environmental stressor. Water quality evaluation along the Conlara River shows deterioration and different types of environmental stressors, identifying zones, and specific sources of pollution. Furthermore, the biomarkers suggest that the native species could be sensitive to anthropogenic environmental pressures.