Most salt marshes in the USA have been degraded by human activities, and coastal managers are faced with complex choices among possible actions to restore or enhance ecosystem integrity. We applied structured decision making (SDM) to guide selection of monitoring variables and management priorities for salt marshes within the National Wildlife Refuge System in the northeastern USA. In general, SDM is a systematic process for decomposing a decision into its essential elements. We first engaged stakeholders in clarifying regional salt marsh decision problems, defining objectives and attributes to evaluate whether objectives are achieved, and developing a pool of alternative management actions for achieving objectives. Through this process, we identified salt marsh attributes that were applicable to monitoring National Wildlife Refuges on a regional scale and that targeted management needs. We then analyzed management decisions within three salt marsh units at Prime Hook National Wildlife Refuge, coastal Delaware, as a case example of prioritizing management alternatives. Values for salt marsh attributes were estimated from 2 years of baseline monitoring data and expert opinion. We used linear value modeling to aggregate multiple attributes into a single performance score for each alternative, constrained optimization to identify alternatives that maximized total management benefits subject to refuge-wide cost constraints, and used graphical analysis to identify the optimal set of alternatives for the refuge. SDM offers an efficient, transparent approach for integrating monitoring into management practice and improving the quality of management decisions.