We analyze the contribution of the Agulhas Current on the central water masses of the Benguela upwelling system (BUS) over the last decades in a high‐resolution ocean simulation driven by atmospheric reanalysis. The BUS is an Eastern Boundary Upwelling System where upwelling of cold nutrient‐rich water favors biomass growth. The two distinct subregions, North and South Benguela, differ in nutrient and oxygen properties of the upwelling water mass. Our analysis indicates that the contribution of Agulhas water to the upwelling is very strong in both subregions. Although the water masses feeding the upwelling have a common origin, their pathways are distinct in both regions. Whereas for the central waters of South Benguela the path is rather direct from where it is formed, the central waters of North Benguela takes a longer route through the equatorial current system. Not only the travel time from the Agulhas Current to the BUS is longer but also the central water mass is twice as old for the northern part when compared to the southern. Our analysis traces the pathways, history, and origin of the central water masses feeding upwelling in the BUS and emphasizes the direct impact of the Agulhas Current on the upwelling region. The variability of that link between the Indian Ocean and the South Atlantic is likely to change the nutrient and oxygen content, as well as temperature and salinity of the water masses in the upwelling region.