ABSTRACT The Delta do Parnaíba Environmental Protection Area (EPA) represents one of the largest deltaic systems in the Americas. This study investigated the spatiotemporal variability of phytoplankton communities and their correlation with environmental factors and assessed their trophic status and water quality across three mesotidal estuaries (Parnaíba-PRE, Comum-CRE, and Bom Gosto-BGRE) over a year-long sampling period. Multivariate analyses explored the interplay between environmental parameters, phytoplankton communities, and trophic indices. Salinity has emerged as a key determinant in these estuaries. Trophic components influence nutrient dynamics, with Redfield ratios indicating colimitation by orthophosphate ( PO 4 3 − ) and silicate ( SiO 2 − ). This study identified 355 taxa within the phytoplankton community, with Chlorophyta predominating in the PRE and diatoms dominating in estuaries with relatively high salinities (BGRE and CRE). Environmental drivers vary across estuaries, with temperature, dissolved oxygen (DO), total nitrogen (TN), chlorophyll-a (Chll-a), and the trophic index (TRIX) influencing the phytoplankton community in the PRE, while salinity, PO 4 3 − , total phosphorus (TP), and TN affect the CRE, and salinity and Chll-a influence the BGRE. The Delta do Parnaíba EPA exhibits eutrophic to hypertrophic conditions, emphasising the need for comprehensive environmental monitoring, nutrient management, and conservation efforts to safeguard biodiversity, water quality, and ecosystem health.