Oyster aquaculture (OA) activity is sometimes framed as a hindrance to habitat, recreation, property values, and wild oyster harvest in Maryland’s Chesapeake Bay. Yet, tradeoffs under OA policies have not been thoroughly analyzed. I applied decision science techniques to capture alternative OA policy effects on users and ecosystem services. Stakeholders helped organize system complexities into management goals and performance indicators and shared preferences to inform indicator weights. These weights were applied to outcomes from a suite of economic and ecological models, resulting in each scenario’s stakeholder-weighted summary score. Results revealed that (1) highly protective habitat policies create a risk to future OA production while protecting less than 0.1% of habitat, (2) proposed changes to current OA policies appear less effective at balancing goals, and (3) under no policy does OA impact more than 1.3% of wild oyster revenues. This analysis served to clarify system complexities to inform policy analysis.