An assessment of the major pigments and neurotoxins and a description of the phytoplankton community were carried out within the coastal region of Rio de Janeiro State (Brazil), during winter and the following spring of 2018. Overall, six stations were investigated for oceanographic conditions (with CTD casts). Filtered water samples were used to estimate the chlorophyll a (CHL-a), carotenoids (CAR), and phycobiliproteins (PHY) using UV–Vis spectrophotometry, as well as the quantification of saxitoxins (STX) and domoic acid (DA), through High Performance Liquid Chromatography (HPLC). Planktonic organisms were counted using sedimentation chambers of different volumes and an inverted microscope. A cluster analysis, SIMPER, and ANOSIM were applied to the phytoplankton data along with diversity indexes, and non-parametric statistics to phycotoxins and pigments. There was a significant difference between the winter and spring phytoplankton community, associated with the mixed layer depth (r2 = −0.626, p < 0.05) and temperature (r2 = 0.641, p < 0.05). Phytoplankton biomass and C:CHL-a indicated a higher production during the winter than in spring, with the potentially toxic genus Pseudo-nitzschia responsible for 12.79% of autotrophic abundance (SIMPER output). Pigments showed a slight increase in CAR during spring, while PHY remained at trace concentrations. Both the DA and STX were quantified in winter and spring, but with significant differences only for STX between the sampling periods. Among the 71 taxa, 11 were identified as potentially toxic with an emphasis on STX-producing dinoflagellates and cyanobacteria, such as Alexandrium sp., Gymnodinium spp. along with Trichodesmium spp. Season-related environmental variability may be the major driving force modulating the mixed assemblage of species that support different levels of phycotoxins.
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