Deltaic and shallow marine sediments represent unique natural archives to study the evolution of surface coastal ocean water properties as compared to environmental changes in adjacent continents. Sea surface temperatures (SSTs) and higher plant biomarker records were generated from the Rhone and Var River deltaic sediments (NW Mediterranean Sea), and three sites in the South Adriatic Sea (Central/Eastern Mediterranean Sea), spanning all or part of the past three millennia. Because of the high sediment accumulation rates at all core sites, we were able to produce time series at decadal time scale. SSTs in the Gulf of Lion and the convection area of the South Adriatic Sea indicate similar cold mean values (around 17°C), and pronounced cold spells, reflecting strong wind‐driven surface water heat loss. However, they differ in the rate of post‐industrial warming, which is steeper in the Gulf of Lion. The three Adriatic Sea SST records are notably different reflecting different hydrological influence from near‐shore to open sea sites. The compositional features of higher plant n‐alkanes in the Rhone and Var delta sediments and inferred vegetation types show differences consistent with the latitudinal extension of the drainage basins of both river‐streams. In the Adriatic Sea, both coastal and open sea sediments indicate enhanced land‐derived material over the past 500 years, that is not seen in the NW Mediterranean cores. We suggest that increased erosion as the result of changes in land use practices is the most likely cause for this trend.