Tidal freshwater zones (TFZs) can significantly affect nutrient transport from watersheds to estuaries through biogeochemical cycling. Phytoplankton, pivotal in nutrient cycling, have been relatively understudied within TFZs. Employing accessory pigment analysis, this study assessed the contribution of diverse phytoplankton groups to chlorophyll a (chl a) biomass over an annual cycle under baseflow conditions. Spatial and temporal patterns in chl a concentrations and community structure as inferred from accessory pigment analysis were evaluated in relation to temperature, dissolved inorganic nitrogen (DIN), soluble reactive phosphorus (SRP), and DIN/SRP ratios. Downstream phytoplankton transport and seasonal succession within the TFZ, driven by nutrient levels and temperature, lead to variations in chl a concentration and community composition. Overall chl a levels were higher in the TFZ than in the upstream river and downstream estuary, with cyanobacteria prominently contributing to chl a biomass, especially in the lower TFZ sections. This study underscores the role of prolonged residence times and nutrient enrichment in TFZs, resulting in elevated chl a concentrations and shaping phytoplankton community composition, with implications for downstream estuaries.