Oceanic mesoscale circulation is a crucial structuring force in the marine environment. Dynamic processes associated with eddies, such as eddy-induced upwelling or eddy-eddy interaction, drive the transport and distribution of nutrients that support the whole food chain, presumably through bottom-up processes. Eddies can shape the distribution of organisms at both low (phytoplankton, zooplankton and fish larvae) and high trophic levels (top fish predators, seabirds or turtles), but the impact of mesoscale features on intermediate trophic levels (micronekton) remains poorly understood. We analysed the influence of eddies on the distribution of micronekton aggregations in the Mozambique Channel by combining data from acoustic surveys and satellite sea topography. We demonstrated that large aggregations of micronekton occurred mainly in areas where the local horizontal gradient of sea level anomalies is strong, i.e. at the periphery of eddies. We observed that, in this region, eddies running along the coast advect coastal nutrient-rich waters at their edges, which support the base of the food chain. We propose that eddies can shape the distribution and the aggregation patterns of the prey of marine top predators through bottom-up processes.