Context and aims A reliable bioindicator index of eutrophication is still lacking for monitoring zooplankton in saline, coastal lagoons. We aimed to establish plankton bioindicators of eutrophication that are not affected by salinity variation, which is essential for environmental monitoring of coastal lagoons. Methods Sampling was conducted for microprotozooplankton, chlorophyll-a, nutrients and sterols in eight tropical coastal lagoons with different saline and nutrient concentrations. A testate amoeba and rotifer bioindication index of eutrophication (T&R index) was proposed after establishing a list of indicator species on the basis of five statistical criteria and one bibliographic criterion. Key results Selected species, based on the six criteria, were Arcella hemisphaerica, Brachionus plicatilis, Galeripora (Arcella) discoides, Netzelia corona, Lecane closterocerca, Lepadela patella and Testudinela patina. Biodiversity measures, traditionally used in biomonitoring, varied negatively with salinity (r = −0.60 for Margalef richness and −0.59 for Shannon diversity) and were not correlated with nutrient concentrations. Conversely, the T&R index showed no correlation with salinity (r = 0.002) and was positively correlated with the trophic-state index (TSI) (r = 0.62). Conclusions and implications Our results showed that specific patterns of indicator microprotozooplankton species can effectively diagnose organic pollution in coastal lagoons and their use is a more suitable approach than is the use of community indicators such as richness, evenness and diversity, traditionally used for that task.