Global change is known to exert a considerable impact on marine and coastal ecosystems, affecting various parameters such as sea surface temperature, rain-off, circulation patterns, and the availability of limiting nutrients like nitrogen, phosphorus and silicon, each influencing phytoplankton communities differently. This study is based on weekly to fortnightly in vivo phytoplankton observations in the French waters of the Eastern English Channel at fine spatial resolution (∼1 km) along an inshore-offshore gradient in the Strait of Dover. Phytoplankton functional composition was addressed by automated ‘pulse shape-recording’ flow cytometry, coupled with 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 μm 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, sea surface temperatures showed an increasing trend in all stations, with nearshore waters warming faster than offshore waters (+1.063 °C vs. +0.929 °C). Changes in nutrient concentrations have led to imbalances in nutrient ratios (N:P:Si) compared to Redfield molar reference ratios, though a rollback (2012–2018) to balanced ratios (since 2019). Phytoplankton total abundance has also increased over the decade, with a higher contribution of small-size cells (picoeukaryotes and picocyanobacteria) and a decrease in microphytoplankton, particularly near the coast. The winters of 2013–2014 and 2019–2020 have been identified as shifting periods in this time series. This study provides the first assessment of decadal changes of the whole phytoplankton community by an automated in vivo single-cell approach, which will need to be explored further in the frame of changes in trophic transfers and water quality.