Inserted in a region known as the Amazon Macrotidal Mangrove Coast (AMMC), the São Marcos Estuarine Complex (SMEC) has presented a scenario of continuous contamination caused mainly by the discharge of domestic, agricultural, and port sewage. Therefore, this study aims to be the first to determine the trophic state of SMEC, assess the ecological status of the phytoplankton community, and apply additive models to investigate the main environmental parameters that drive phytoplankton. Collections were carried out during the dry season (September and December/2018) and the rainy season (March and June/2019). Seasonal influence on environmental and biological factors was observed, especially those used to classify water quality. Based on the Multimetric Trophic Index (TRIX), SMEC was classified as eutrophic, and the general nutritional status of phytoplankton revealed that the system was predominantly nitrogen-limited. The phytoplankton community was dominated by diatoms, with emphasis on the presence of potentially harmful species such as Pseudo-nitzschia pungens, Coscinodiscus centralis, Thalassiosira subtilis and Skeletonema costatum, which can cause ecological and economic losses in the environment. Such species contributed to the low diversity and moderate richness. Hydrological variables such as temperature, salinity, and turbidity, in addition to nutrients, especially nitrate and phosphate, were the main parameters controlling phytoplankton structure and abundance, revealing an indicator community well adapted to local conditions. Overall, the integrated study of trophic and ecological indices in the SMEC appeared to be sensitive to changes in water quality, being an efficient tool to indicate the current scenario of this environment.
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