AbstractAs in many other countries, Peru has the Water Quality Standard (WQS) as the primary tool for managing and diagnosing water resources. An analysis of variable by variable was applied to define water quality as poor or good by setting concentration limits. A second group of tools commonly used are Biotic Indexes based on tolerance of benthic macroinvertebrates to pollution, that reflect the impacts caused by a group of variables, even though they cannot identify which variables determine the viability of the ecosystem. This research proposes to include the Stable States approach to evaluate the ecological integrity in central‐Andes rivers to explore an alternative approach with the capacity to represent a broader number of factors through multivariate analyses. A ten‐year database of biological, physical, and chemical variables measured in five Andean Rivers was evaluated. Our results suggest these rivers fluctuate into two seasonal stable states (wet and dry season), accounting for approximately 41% of the system variability. The wet season stable state was defined by high levels of suspended solids and turbidity, coliform, phosphorus, and some metals. During the dry season, the key variables were dissolved solids, barium, pH, and dissolved oxygen. Likewise, there seems to be a third alternative state influenced by human pressures driven by organic pollution variables that exceed the WQS. Regarding water quality, the concentrations of coliforms, phosphorus, and lead usually exceeded the limits in two stations, but not every year. Between bioindicator indexes, the ABI represented the ecological condition more accurately than EPT.