Coastal marine ecosystems, which play a crucial role in the biogeochemical and ecological functioning of the Earth, are highly sensitive to the combined effects of climate and human activities. Because of their location, coastal ecosystems are directly influenced by human activities, but it remains challenging to assess the spatial and temporal scales at which climate influences coastal ecosystems. We monitored 12 sampling stations, distributed in 8 ecosystems in France, over 2 decades for physico-biogeochemical parameters (temperature, salinity, concentrations of dissolved oxygen, nutrients and particulate material). The study encompasses a large diversity of temperate coastal ecosystems with respect to e.g. geomorphology, trophic status, tidal regime, river influence and turbidity. Time-series analysis coupled with standardised 3-mode principal component analyses, partial triadic analyses and correlations were used to assess bi-decadal variability and ecosystem trajectories, and to identify large-scale, regional and local drivers. Our results highlighted 2 abrupt changes in 2001 and 2005. The bi-decadal changes were related to changes in large-scale and regional climate, detected through proxies of temperature and atmospheric circulation, as well as through river discharge. Ecosystem trajectories tended to move towards an increase in temperature and salinity, and/or a decrease in chlorophyll a, nutrients and particulate matter. However, the magnitude of change, the year-to-year variability and the sensitivity to the 2001 and 2005 changes varied among the ecosystems. This study highlights the need for establishing long-term time series and combining data sets as well as undertaking multi-ecosystem and local studies to better understand the long-term variability of coastal ecosystems and its associated drivers.