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The phytoplankton functional composition was addressed by automated “pulse-shape recording” flow cytometry, coupled with the analysis of environmental variables over the last decade (2012–2022). This method allows for the characterization of almost the entire phytoplankton size range (from 0.1 to 800 µm width) and the determination of the abundance of functional groups based on optical single-cell signals (fluorescence and scatter). We explored seasonal, spatial and decadal dynamics in an environment strongly influenced by tides and currents. Over the past 11 years, the SST has shown an increasing trend at all stations, with nearshore waters warming faster than offshore waters (+1.05 °C vs. +0.93 °C). Changes in nutrient concentrations have led to imbalances in nutrient ratios (N:P:Si) relative to reference nutrient ratios. However, a return to balanced ratios has been observed since 2019. The phytoplankton total abundance has also increased over the aforementioned decade, with a higher contribution of small-sized cells (picoeukaryotes and picocyanobacteria) and a decrease in microphytoplankton, particularly near the coast. Based on an analysis of environmental parameters and phytoplankton abundance, the winters of 2013–2014 and 2019–2020 were identified as shifting periods in this time series. 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