The data submitted here is published in the manuscript entitled "On-shelf nutrient trapping enhances fertility of the southern Benguela upwelling system". Our data show that regenerated nutrients get “trapped” on the shelf of the southern Benguela upwelling system (SBUS), increasing the on-shelf nutrient pool available for upwelling. Nutrient trapping occurs when phytoplankton consume upwelled nutrients, sequestering them in their biomass, then sink and are decomposed on the shallow continental shelf, releasing nutrients to bottom waters. The nutrient-deplete surface waters subsequently flow offshore. SBUS nutrient trapping appears to be assisted by hydrographic fronts that limit the offshore transport of phytoplankton, such that their sinking and subsequent decomposition occurs on-shelf. Decomposition consumes oxygen, which means that enhanced nutrient trapping may increase oxygen depletion in the SBUS, with ecosystem-wide deleterious effects.