AbstractShifts in the phytoplankton assemblage induced by environmental changes have significant implications for carbon cycling and marine food webs, but remain poorly constrained across spatiotemporal scales. Here, we investigate the effects of rising sea surface temperatures and increased stratification on the phytoplankton composition and size in the northwestern Mediterranean Sea (2010–2019) using two sediment trap series: one in the oligotrophic Ligurian Sea and the other in the deep convection zone of the Gulf of Lion. We apply deep learning image analysis to quantify phytoplankton particle fluxes, size distributions, and relative assemblages, focusing on coccolithophores, diatoms, and silicoflagellates. Our results show a general decline of phytoplankton fluxes to the seafloor, mirroring the decrease in vertical mixing in the water column. Both sites show a shift toward phytoplankton species adapted to stratified and nutrient‐depleted conditions, although with contrasting patterns. In the Ligurian Sea, deep‐dwelling coccolithophore species become dominant, while in the Gulf of Lion, summer‐associated siliceous species, including large diatoms and silicoflagellates, show an increase. These contrasted trends, which likely result from differences in nutrient inputs and pH changes in the surface between the two sites, have implications for the efficiency of carbon export pathways at depth. Specifically, the increasing dominance of smaller phytoplankton in the Ligurian Sea leads to a reduction in carbon burial efficiency, while in the Gulf of Lion, the enhanced contribution of larger diatoms may sustain higher export and burial rates in the future.