The complexity of ecological-economic systems significantly reduces our ability to investigate their behavior and propose policies aimed at various environmental and/or economic objectives. Following recent suggestions for integrating nonlinear dynamic modeling with input-output (IO) modeling, we develop a fully dynamic ecological-economic model by integrating IO with system dynamics (SD) for better capturing critical attributes of ecological-economic systems. We also develop and evaluate various scenarios using policy impact and policy sensitivity analyses. The model and analysis are applied to the degradation of fish nursery habitats by industrial harbors in the Seine estuary (Haute-Normandie region, France). The modeling technique, dynamization, and scenarios allow us to show trade-offs between economic and ecological outcomes and evaluate the impacts of restoration scenarios and water quality improvement on the fish population.