β-diversity and functional traits of phytoplankton indicators associated with environmental heterogeneity were investigated as environmental quality descriptors in coastal (CS), estuarine (ES), and limnetic (LS) sectors in a tropical river-to-sea ecosystem. Results showed that environmental heterogeneity was marked by spatial differences, contributing to biological heterogeneity. Sporadic and recurrent blooms were associated with environmental spatiotemporal variations and reflected a reduction in ES α-diversity. Salinity acted as an environmental filter that governed the structure and dynamics of the community. The spatial heterogeneity and high turnover of phytoplankton resulted in reliable bioindicators selection. Colonial, bloom-forming and harmful species were associated with highly suspended particulate matter (SPM) because these species are better adapted to these conditions. Species small in size were associated with high concentrations of silicate and chlorophyll-a in the ES because of the occurrence of diatom recurrent blooms. Most flagellates indicators genera have bloom-forming potential. Integrating morphofunctional with taxonomic approaches enabled detailed observations of environmental filters, supporting the selection of priority species and areas for introducing biodiversity monitoring programs and conservation in tropical ecosystems.