Aerial surveys of coastal habitats can uniquely inform the science and management of shallow, coastal zones, and when repeated annually, they reveal changes that are otherwise difficult to assess from ground-based surveys. This paper reviews the utility of a long-term (1984–present) annual aerial monitoring program for submersed aquatic vegetation (SAV) in Chesapeake Bay, its tidal tributaries, and nearby Atlantic coastal bays, USA. We present a series of applications that highlight the program’s importance in assessing anthropogenic impacts, gauging water quality status and trends, establishing and evaluating restoration goals, and understanding the impact of commercial fishing practices on benthic habitats. These examples demonstrate how periodically quantifying coverage of this important foundational habitat answers basic research questions locally, as well as globally, and provides essential information to resource managers. New technologies are enabling more frequent and accurate aerial surveys at greater spatial resolution and lower cost. These advances will support efforts to extend the applications described here to similar issues in other areas