Water quality in the Chesapeake Bay has decreased since the 1950s due to an increase in nutrient loadings that have increased the extent and duration of hypoxic conditions. Restoration via large-scale reductions in nutrient loadings is now underway. How reducing nutrient loadings will affect water quality is well predicted; however, the effects of reduced nutrients (reduced food availability) and associated reduced hypoxia on fish are generally unknown as most water quality models do not include trophic levels higher than zooplankton. We dynamically coupled a spatially explicit, individual-based population dynamics model of juvenile and adult anchovy to the three-dimensional Chesapeake Bay eutrophication model. Growth rates of individual anchovy were calculated using a bioenergetics equation. Anchovy consumption rates were forced by zooplankton densities from the water quality model, and anchovy consumption of zooplankton was added as an additional mortality term on zooplankton in the eutrophication model. Anchovy mortality was size dependent and their movement depended on water temperature, dissolved oxygen, and zooplankton concentrations. Multi-year simulations with fixed annual recruitment were performed under decreased, baseline, and increased nutrient loadings scenarios. The results of our analyses show that anchovy responses to changed nutrient loadings are dominated by changes in productivity, including simultaneous changes in growth and mortality rates, and spatial distribution, and depend on life stage. As such, we recommend using full life cycle, spatially explicit population models that are dynamically coupled to water quality models as a tool for predicting the effects of changes in nutrient loadings on fish population dynamics.