Abstract
The alpha diversity and environmental heterogeneity of zooplankton reflect the level of degradation in a macrotidal estuary on the Brazilian equatorial margin. Using the multimetric index (TRIX), we assessed the trophic state and its association with zooplankton composition, distribution, and environmental variables in a tropical estuary. The results showed that significant seasonal and sectoral environmental differences contributed to biological heterogeneity, with the second sector (SII) exhibiting the greatest impact, leading to decreased alpha diversity compared to that of the first sector (SI). Salinity, pH, SiO23, and NO2− exhibited significant seasonal and sectoral variations (p < 0.05). The community consisted of 74 taxa, with copepods (75.7%), mainly from Oithonidae and Paracalanidae, dominating species number. Overall, the community exhibited medium diversity, low richness, and heterogeneity. Beta diversity, calculated using PERMADISP and Jaccard dissimilarity, reflected environmental heterogeneity with significant seasonal differences and biological variability between rainy and dry periods. Indicator species analysis identified 15 taxa, including copepods such as Euterpina acutifrons and Clytemnestra scutellata. Of these, nine taxa (60%) were indicators for the SI, and six (40%) were indicators for the SII. This study underscores the importance of identifying environmental filters and indicator species to understand estuarine dynamics and assess ecosystem trophic states.