The northern Benguela ecosystem has been overfished and physically challenged over the past three decades. Ecopath with Ecosim was used to construct three ecosystem models (1971–1977, 1980–1989, and 1990–1995) and to compare differences in ecosystem structure. In the 1970s, the system sustained high catches, and had large populations of a few planktivorous fish. In the 1980s, the planktivorous fish species were expanded (horse mackerel, mesopelagic fish, and other small pelagics), although anchovy and sardine biomass was reduced. Catches remained high in the 1980s and the system was well connected. In the 1990s, the system was severely stressed, catches were much lower and omnivory was reduced. Most of the energy flowed through few pathways in the 1990s, and the energy was not transferred as efficiently up the trophic chain as in the 1980s. The fishery operated at the highest trophic level during the 1980s and there are some indications of “fishing down the foodweb” in this ecosystem between the 1980s and the 1990s. The high catches of sardine and hake in the 1970s are reflected in the high primary production required (PPR) by those compartments; the high catches of horse mackerel in the 1980s are shown by the high PPR for horse mackerel. The overall PPR for the fishery was highest in the 1980s, when the system was fished at nearly the same intensity as the 1970s, but the species taken were from higher trophic levels, requiring larger concentrations of primary production for their own existence. The importance of ecosystem–environmental interactions are highlighted by the abundance of horse mackerel, mesopelagics, small pelagics, and hake in the 1980s and the reduced biomass of most species in the 1990s, not only due to overfishing, but also due to the Benguela Niño that occurred in 1995. The system changed from an efficient ecosystem dominated by only two planktivores (anchovy and sardine) in the 1970s, to a system of large resilience and a varied planktivore population during the 1980s. However, the system’s resilience was lower, but its connectance was higher in the 1990s, where sardine was making a comeback and the marine mammals were doing well until the Benguela Niño reduced the system to a state of lower maturity.