Abstract Worsening marine hypoxia has had severe negative consequences for fish communities across the globe. While individual and populationlevel impacts of deoxygenation have been identified, it is unknown how they interact to drive changes in food webs. To address this, we incorporated several major impacts of hypoxia, including declines in benthic re sources, habitat shifts, increasing mortality, and changes to rates of feeding, assimilation, and reproductive efficiency, into an existing size spectrum food web modeling framework. We used this structure to ask the following questions: which of these direct effects are most critical to capturing population and community dynamics in a representative hypoxic system, how do they interact to result in community responses to deoxygenation, and what are the potential consequences of these effects in the context of accelerating deoxygenation? We tested the effect of different combinations of oxygendependent processes, driven by observed oxygen levels, on the food web model’s ability to explain time series of observed somatic growth, diets, biomass, and fishery yields of commercially relevant species in the Baltic Sea. Model results suggest that food availability is most critical to capturing observed dynamics. There is also some evidence for oxygendependent habitat use and physological rates as drivers of observed dynamics. Deoxygenation results in declining growth both of benthic and benthopelagic fish species, as the latter are unable to compensate for the loss of benthic resources by consuming more pelagic fish and resources. Analysis of scenarios of ideal, declining, and degraded oxygen conditions show that deoxygenation results in a decline in somatic growth of predators, an altered habitat occupancy resulting in changing species interactions, and a shift in energy flow to benthopelagic predators from benthic to pelagic resources. This may have important implications for management as oxygen declines or improves.