Oceanic mesoscale eddies are energetic features where strong three-dimensional circulations are set up and consequently enhanced biological activity take place. Indeed, vertical circulation associated with mesoscale eddies is of great importance as it may explain the patchiness of chlorophyll in the surface layers of the ocean. The E-MOTION project is focused on the estimation and analysis of the vertical exchanges associated with mesoscale dynamics and of their interannual variability, concentrating on selected areas of the World Ocean. The rationale for this project comes, on one hand, from the fundamental role played by the mesoscale in modulating ocean circulation and the fluxes of heat, freshwater and biogeochemical tracers between the surface and the deeper layers and, on the other hand, from the high level of uncertainty related to the possible feedbacks from mesoscale variability on both Earth climate and marine ecosystem functioning. The approach chosen to achieve the E-MOTION objective presents several original and innovative elements: (1) applying a quasi-geostrophic (QG) diagnostic to new model and observational products, (2) comparing its results with corresponding primitive equation solutions, (3) investigating the potential links between QG vertical motion and surface chlorophyll using tools for eddy identification and tracking, and (4) exploring alternative mechanisms of vertical motion that may affect ecosystem dynamics. E-MOTION will contribute towards improving our understanding of the net effect of mesoscale variability on water mass formation and transport at the global scale, as well as on its impact on biochemical tracer redistribution and consequent marine ecosystem response.