Designing effective spatial management strategies is challenging because marine ecosystems are highly dynamic and opaque, and extractive entities such as fishing fleets respond endogenously to ecosystem changes in ways that depend upon ecological and policy context. We present a tool, `marlin`, that can be used to efficiently simulate the bio-economic dynamics of marine systems in support of both management and research. We demonstrate `marlin’s` capabilities by focusing on two case studies on the conservation and food production impacts of marine protected areas (MPAs): a coastal coral reef and a pelagic tuna fishery. In the coastal coral reef example, we explore how heterogeneity in species distributions and fleet preferences can affect distributional outcomes of MPAs. In the pelagic case study, we show how our model can be used to assess the climate resilience of different MPA design strategies, as well as the climate sensitivity of different fishing fleets. This paper demonstrates how intermediate complexity simulation of coupled bio-economic dynamics can help communities predict and potentially manage trade-offs between conservation, fisheries yields, and distributional outcomes of management policies affected by spatial bio-economic dynamics.