The Tunuyán and Mendoza River Basins (Province of Mendoza, Argentina) have been selected as a representative semiarid region to test the applicability of an integrated water quality evaluation. To detect spatio-temporal variations of anthropic contamination, physicochemical and bacteriological parameters, as well as three ecotoxicological assays, were assessed in reference sites for 3years. Bioassays based on the nematode Caenorhabditis elegans, the vascular plant Lactuca sativa, and the algae Pseudokirchneriella subcapitata were performed and toxicological categories were established. Our results showed that water quality, as well as water toxicity, deteriorates as both river systems run through urban areas. Interestingly, monitoring sites with good physicochemical and bacteriological qualities but with toxicity were identified, illustrating that traditional water quality studies do not predict potential toxic effects on living organisms. In addition, a multivariate statistical analysis was performed to detect clusters of monitoring sites according to the water quality status. In the context of climate change, this study provides information to support that integrated water monitoring is an essential tool to ensure sustainable water management and to guarantee economic growth, human health, food security, and environmental protection.