Eddies play a crucial role in shaping ocean dynamics by affecting material transport, and generating spatio-temporal heterogeneity. However, how eddies at different scales modulate biogeochemical transformation rates remains an open question. Applying a multi-scale decomposition to a numerical simulation, we investigate the respective impact of mesoscale and submesoscale eddies on nutrient transport and biogeochemical cycling in the California Current System. First, the non-linear nature of biological nutrient uptake results in a 50% reduction in primary production in the presence of eddies. Second, eddies shape the vertical transport of nutrients with a strong compensation between mesoscale and submesoscale. Third, the eddy effect on nutrient uptake is controlled by the covariance of temperature, nutrient and phytoplankton fluctuations caused by eddies. Our results shed new light on the tight interaction between non-linear fluid dynamics and ecosystem processes in realistic eddy regimes, highlighting the importance of both mesoscale and submesoscale variability.