The response of phytoplankton to various ecological forcings has been examined in the upper waters of the NW Mediterranean (MED) and the subtropical North Atlantic (NA). Particular emphasis was given to the role played by the water column structure in controlling the vertical nitrogen diffusion and new production. 1. The spring microplankton metabolism of surface mixed waters in a narrow-shelf area of MED was assessed. An overall heterotrophic metabolism was found to prevail at the time of the study, explained by high rates of dark community respiration attributed to the late consumption of the organic matter excess produced in winter and accumulated in the mixed layer. 2. Summer primary production and nitrogen fluxes in stratified water layers in NA were evaluated. The nitrogen flux fuelling new primary production was closely linked to vertical turbulent diffusion at the nitracline rather than at the thermocline. The vertical turbulent diffusion model did not explain the new production in the Canary Current zone, where laterally advected nutrients from coastal upwelling areas altered the vertical nitrate gradients. 3. A nitrogen-based vertically resolved ecological model simulating upper and intermediate waters of the open ocean was developed to assess the plankton response to different conditions of irradiance, mixed-layer depth, and nitrogen concentration below the euphotic zone. 4. Using the model, a comparative study between MED and NA was carried out. The nitrate entering the euphotic zone through the lower boundary explained the phytoplankton and zooplankton stocks variability in both ecosystems. The balance of light availability and nutrient concentration controlled the chlorophyll maximum depth, independently of density. The zooplankton grazing prevented this maximum to reach higher concentrations. Simulations of phytoplanktonic dark nitrate reduction and exudation were coincident with previous observations elucidating the nitrite maximum. Estimates of turbulent diffusion from density explained the upward-downward nitrogen flux in both ecosystems assumed to be near the yearly metabolic balance.