We validated simulations of the Earth system model (ESM) EC-Earth-NEMO of present-day temperature, salinity, nutrient, and chlorophyll a profiles with in situ observations in the Northeast Atlantic Ocean (29–63º N). Simulations with standard parametrization (run 1) and improved parametrization of vertical mixing (run 2) were compared. Run 1 showed shallower mixed layer depths (MLDs) in spring as compared to observations owing to lower salinities in the upper 200 m of the subpolar North Atlantic (>55º N). This coincided with a mismatch with observed timing and magnitude of the phytoplankton spring bloom. In contrast, the model performed well south of 55º N. Run 2 showed improved springtime MLD, phytoplankton dynamics, and nutrient distributions in the subpolar North Atlantic. Our study underlines the sensitivity of subpolar North Atlantic phytoplankton blooms to surface freshening, suggesting that future fresh-water inflow from Arctic and Greenland Ice sheet melting could significantly affect phytoplankton productivity. These findings contribute to the generic validation of the EC-Earth ESM and underline the need for rigorous validation of physics-biology links, in particular the sub polar North Atlantic where complex seasonal stratification/vertical mixing processes govern upper ocean phytoplankton productivity.