The decline in the water quality of water resources in the Amazon is very rapid in cities that suffer from unplanned urban growth. The region has two defined seasons, winter (wet) and summer (dry), which directly affect the behavior of contaminants in aquatic ecosystems. This study aimed to assess the ecological and human health risks associated with the use of microbasin. In addition, the ecological indices were proposed: the Quality Index for Aquatic Life, for the risk of contaminants to aquatic life. Sampling was performed at six sampling points in the Juá microbasin. Physicochemical parameters, major anions, metals, and total phosphorus were analyzed at both stations between 2020 and 2021. The highest concentrations of contaminants were found in the rainy season, as Cl presented a concentration more than 307 times that allowed by the Brazilian legislation. The ecological index showed that the microbasin has a high risk of metals such as Cr III and Cr VI hazard the biota. The human health risk analysis showed a low risk; however, the lack of basic sanitation in the city indicates that monitoring urban water resources is necessary.