The Albufera of Valencia is a hypereutrophic, oligohaline lagoon that has experienced significant changes in phytoplankton composition and state in recent decades due to human activities. These activities affect phytoplankton biomass and community structure, which are key indicators of ecosystem health. In this study, phytoplankton samples from the lagoon were analyzed to identify dominant groups and genera, and their seasonal cycles were determined using biovolume measurements with the Utermöhl method. Various environmental variables were also measured. Diversity was assessed using richness, equitability, and the Shannon–Wiener index. Canonical Correspondence Analysis (CCA) and Pearson correlation revealed that temperature and phosphorus significantly influence phytoplankton abundance. A species that exhibited seasonal abundance, resulting in a change in the lagoon’s color from green to brown, was identified. Water quality was assessed using the trophic state index, indicating that the lagoon is in poor condition and hyper-eutrophic. Cyanobacteria were the most dominant group, peaking in November, contrary to previous studies, followed by Chlorophyceae and Bacillariophyceae. Phytoplankton are vital bioindicators for assessing ecosystem health, underscoring the need for further research in this area.
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