This paper presents a new, updated, temporally dynamic Ecosim model for the Southern Benguela (1978–2015) by capturing recent advancements in our understanding of the dynamics and newly available data series from an additional decade of research in the region. The paper documents the model development and the thinking behind incorporating a newly available upwelling index, and observed fishing effort as important drivers of modeled ecosystem dynamics. The most sensitive predator-prey interactions were identified and vulnerabilities (of prey to predators) were estimated to improve model fit to field observations under each scenario. Sardine interactions with prey and predators were consistently found to be sensitive interactions in model fitting, accounting for at least 40% of the most sensitive trophic interactions in the southern Benguela modeled food web. Model fits to data were improved by a total of 85% reduction in sum of squares when upwelling effects on large phytoplankton availability to zooplankton and small pelagic fish was incorporated, geographic shifts in sardine distribution were captured by means of altered availability of sardine to predators, corresponding vulnerabilities of prey to predators were estimated, and an additional, small, hypothetical forcing function was fitted to small phytoplankton production. African penguin and Cape gannet fits to data series were improved by incorporating a recently published bird Food Availability Index, although model fits of several fish groups then deteriorated, emphasizing the need for additional empirical species-specific functional response studies. Attempts at fitting the full area model to either west coast or south coast time series did not improve overall model fits, highlighting limitations of the current non-spatialized model in describing coast-specific dynamics. This study shows promise in unraveling the observed dynamics of the Benguela upwelling ecosystem, and points to the importance of exploring spatially disaggregated approaches, in particular the new foraging habitat capacity of the Ecospace approach, to improve our understanding of processes whereby variability in upwelling influences dynamics of the Southern Benguela ecosystem. This is important in reconciling knowledge needed to manage fisheries and to protect marine biodiversity by means of ecosystem-based management in South Africa, and to advance management advice under future scenarios of climate change.