Urban coastal wetlands and adjoining coves and embayments can provide habitat for significant numbers of waterbirds, despite being subject to high levels of stressors from human activities. Yet to date little emphasis has been placed on identifying these areas and prioritizing them for conservation. In this study I outline a three-step process to identify and prioritize local sites for conservation using waterbird abundance and diversity and an index of the risk to a site from marine development, and apply it to a series of urban coastal sites in two North Atlantic estuaries located in the northeast US. By combining waterbird abundance and species richness with the risk from marine development I generated a ranked list of sites with the highest listed sites having high bird diversity and low risk from development. From this list individual sites can be prioritized for conservation, and various protection scenarios can be evaluated and compared. For example, 7 of the top 10 ranked sites in Boston Harbor, combined with sites already protected under local, state, or federal statutes, represented over half of the total bird diversity in the Harbor. Similarly, in Narragansett Bay 6 of the top 10 sites when combined with sites already protected represent 48.8% of the Bay's bird diversity. Formally protecting these sites, all of which are at relatively low risk from marine development, could result in the conservation of considerable waterbird habitat at low economic cost (i.e., from loss of development potential). Other ranking scenarios (by bird diversity alone, or by risk from marine development) were also evaluated and compared to the combined ranking. Identification of sites with high bird diversity and low risk from development could provide important information for local land acquisition groups and planning boards when considering options for the conservation of urban coastal habitats.