and microbiological parameters were measured and integrated using the Water Quality Index of the Canadian Council of Ministers of the Environment. Ecotoxicological tests were performed with Brazilian endemic organisms to assess the impact of water pollution on biota. A generalized linear regression model was applied to understand the effects of water quality on ecotoxicological responses. Concentrations of metals, dissolved oxygen, total ammonia nitrogen, nitrate, and thermotolerant coliforms did not comply with Brazilian environmental regulations. A significant increase in the mortality rate of Mysidopsis juniae and Nitocra sp. and a significant decrease in the reproductive rate of Nitocra sp. indicated the most affected areas related to the discharge of treated and untreated wastewater. Only 10% of the samples from sites without direct wastewater impact showed a toxic response in at least one organism. Both water quality and sampling sites were statistical predictors of ecotoxicological response, describing not only the pollutant load but also the type of effluent. This study demonstrated the degradation of the environmental quality of the JPE, particularly due to the discharge of sanitary wastewater, and highlights the importance of protection and remediation measures to preserve this protected area.