Single species approaches to natural resource conservation and management are now viewed as antiquated and oversimplified for dealing with complex systems. Scientists and managers who work in estuaries and other marine systems have urged adoption of ecosystem based approaches to management for nearly a decade, yet practitioners are still struggling to translate the ideas into practice. Similarly, ecological restoration projects in coastal systems have typically addressed one species or habitat. In recent years, efforts to focus on multiple species and habitats have increased. Our project developed an integrated ecosystem approach to identify multi-habitat restoration opportunities in the Great Bay estuary, New Hampshire. We created a conceptual site selection model based on a comparison of historic and modern distribution and abundance data, current environmental conditions, and expert review. Restoration targets included oysters and softshell clams, salt marshes, eelgrass beds, and seven diadromous fish species. Spatial data showing the historical and present day distributions for multiple species and habitats were compiled and integrated into a geographic information system. A matrix of habitat interactions was developed to identify potential for synergy and subsequent restoration efficiency. Output from the site selection models was considered within this framework to identify ecosystem restoration landscapes. The final products of these efforts include a series of maps detailing multi-habitat restoration opportunities extending from upland freshwater fish habitat down to the bay bottom. A companion guidance document was created to present project methods and a review of restoration methods.