This study uses Cu and Zn isotopic compositions as proxies of sources and metal transfers in the planktonic food webs from the Mediterranean Sea. Plankton was collected in spring 2019 in the deep chlorophyll maximum (DCM) along a North-South transect including coastal and offshore zones (MERITE-HIPPOCAMPE campaign). δ65Cu and δ66Zn were determined on four planktonic size fractions from 60 to 2000 μm. Combined δ65Cu and δ66Zn with geochemical tracers (Ti, particulate organic phosphorus) showed that geogenic particles were ubiquitous with plankton assemblages. The δ15N ecological tracer showed that planktonic food web was enriched in heavy isotopes of Cu and Zn in the higher trophic levels. δ65Cu were correlated with picoplankton in the offshore zone, and with zooplankton in the southern coastal zone. Firmicutes bacteria were found correlated with δ66Zn in northern and southern coastal zones suggesting decomposition of particulate matter at the DCM. These findings suggest that biogeochemical process may impact Cu and Zn isotopy in the planktonic community.