Knowledge of the relative contributions of phytoplankton size classes to zooplankton biomass is necessary to understand food‐web functioning and response to climate change. During the Deep Water formation Experiment (DEWEX), conducted in the north‐west Mediterranean Sea in winter (February) and spring (April) of 2013, we investigated phytoplankton‐zooplankton trophic links in contrasting oligotrophic and eutrophic conditions. Size fractionated particulate matter (pico‐POM, nano‐POM, and micro‐POM) and zooplankton (64 to >4000 μm) composition and carbon and nitrogen stable isotope ratios were measured inside and outside the nutrient‐rich deep convection zone in the central Liguro‐Provencal basin. In winter, phytoplankton biomass was low (0.28 mg m−3) and evenly spread among picophytoplankton, nanophytoplankton, and microphytoplankton. Using an isotope mixing model, we estimated average contributions to zooplankton biomass by pico‐POM, nano‐POM, and micro‐POM of 28, 59, and 15%, respectively. In spring, the nutrient poor region outside the convection zone had low phytoplankton biomass (0.58 mg m−3) and was dominated by pico/nanophytoplankton. Estimated average contributions to zooplankton biomass by pico‐POM, nano‐POM, and micro‐POM were 64, 28 and 10%, respectively, although the model did not differentiate well between pico‐POM and nano‐POM in this region. In the deep convection zone, spring phytoplankton biomass was high (1.34 mg m−3) and dominated by micro/nano phytoplankton. Estimated average contributions to zooplankton biomass by pico‐POM, nano‐POM, and micro‐POM were 42, 42, and 20%, respectively, indicating that a large part of the microphytoplankton biomass may have remained ungrazed.