Ecosystem-based fisheries management calls for the consideration of the indirect and cumulative effects of fishing, in addition to estimating direct fishing mortality. Here, we quantify such effects of fishing fleets, and their interactions, using a spatially explicit Atlantis simulation model of the food web and fisheries in the California Current. Simulations testing the effects of single fleets suggested that bottom trawl, fixed gear, and hake (Merluccius productus) trawl primarily have direct impacts on their target and bycatch species. Few indirect effects from these three fleets extended through predator–prey links to other parts of the food web. In contrast, effects of the purse seine fleet extended beyond the three groups it harvested, strongly altering the abundance of predators, planktonic prey, and benthos. In terms of nine ecosystem attributes, our experiments involving single fleets identified six fleets that caused the bulk of negative impacts. Specific fleets impacted different aspects of the ecosystem, for instance with groundfish gears causing reductions in piscivore abundance, and hake trawl and purse seine increasing krill through reducing abundance of planktivores. In terms of interactions among fleets' effects, the vast majority of effects were simply additive – the combined effect of two fleets was simply the sum of the individual fleets' effects. The analyses offer one way to sharpen the focus of ecosystem-based fisheries management in the California Current, emphasizing impacts and interactions of particular stressors.