Estuaries are extremely valuable ecosystems and have been affected by several anthropogenic activities from urban growth and industrial development, such as the release of untreated effluents which decrease water quality. This study aimed to evaluate the seasonal and temporal trophic status variation in the Formoso River Estuarine System (FRES), a tropical estuary. Three campaigns were carried out in each season (rainy and dry), during which surface water was sampled for abiotic parameter analyses. The TRIX index was used for trophic status assessment. For the temporal evaluation, a review of literature addressing the matter in the study area was conducted. Between 2017 and 2018, the TRIX index varied from a mean of 6 ± 0.2 upstream to 5 ± 0.4 downstream during the rainy season, indicating eutrophic conditions throughout most of the FRES extension, especially near the Formoso River, and from 6 ± 1 to 3 ± 0.8 during the dry season. Temporal analyses showed that in 2002 the overall mean TRIX index was 5.72 ± 0.4, decreasing in 2005 and 2014, and followed by an upwards trend. We conclude that the FRES is impacted by the release of untreated effluents such as sewage and fertilizers from the city of Rio Formoso and from various agricultural activities, which are more intense during the rainy season. Nevertheless, over time there were more critical scenarios pertaining to the trophic status. The present diagnosis reinforces the importance of public sanitation policies in estuarine regions and spatial planning instruments for pollution control in fishery areas.