Long-term trends in the phytoplankton community along the French coast of the English Channel and southern Bight of the North Sea were studied and related to physico-chemical factors and large-climatic indices. Phytoplankton and hydrological data were acquired through three transects. Sampling took place between 1992 and 2011 as part of the French Phytoplankton Monitoring Network (REPHY) and the Regional Nutrients Monitoring Network (SRN). Trends in time-series were identified with dynamic linear models tailored to environmental monitoring data characteristics (e.g. irregular sampling frequency, missing data). Temporal and spatial patterns in the phytoplankton community were explained with a partial triadic analysis. Relationships between the phytoplankton community composition, environmental factors, and climatic indices were assessed using a redundancy analysis (RDA). The analyses revealed long-term changes in the community composition, characterized by a temporal structure that remained common to all transects. The abundance of some groups of taxa such as the one composed by Gymnodinium and Gyrodinium, as well as the group of Pseudo-nitzschia increased during the study period, whereas the abundance of other taxa as for example Guinardia and the group of Coscinodiscus and Stellarima globally decreased. More generally, the proportion of dinoflagellates relative to diatoms increased. Trends in environmental variables were also observed in most sites and related to decreases in nutrient concentrations and an increasing trend in salinity. The RDA indicated that the Atlantic Multidecadal Oscillation index and salinity were the main factors defining the temporal structure of the phytoplankton community. This suggests that variations observed in the phytoplankton community are linked to hydro-climatic changes in the coastal environment.