Spatial and temporal distribution patterns of zooplankton are highly variable in the Northern Benguela Upwelling System. We studied the distribution of zooplankton (size class ≥ 0.33 mm) and used field data from four cruises that took place between March 2008 and February 2011, as well as simulation results of a regional ecosystem model. Remotely sensed sea surface temperatures (SST) and surface chlorophyll concentrations were analysed to investigate environmental influences on zooplankton biomass. The Intense Benguela Upwelling Index showed a distinct seasonal signal throughout the years and the highest upwelling peaks in August/September. Even though surface chlorophyll concentrations were very variable throughout the year, the highest concentrations were always detected in September, following the upwelling of nutrient-rich water. In field catches, zooplankton biomass concentration in the upper 200 m was highest above the outer shelf and shelf-break in December 2010 and February 2011, i.e. 6 months after the upwelling peaks. In contrast, zooplankton biomass simulated by the model in the surface water was highest in September. In March/April, biomass maxima were typically measured in the field at intermediate water depths, but the vertical distribution was also affected by extensive oxygen minimum zones. The ecosystem model reproduced this vertical pattern. Although general trends were similar, simulation data of zooplankton standing stocks overestimated the field data by a factor of 3. In upwelling systems, food webs are generally considered to be short and dominated by large cells. However, our field data indicate more small-sized zooplankton organisms above the shelf than offshore.