A variety of factors influence water quality in the ocean and bays surrounding Assateague Island. Perhaps most significantly, the adjacent mainland is undergoing rapid population growth, resulting in a variety of stresses to local aquatic environments. Ocean City, Maryland, lying directly north of the island, is a large, extensively developed resort area accommodating millions of visitors during the summer months. Maryland's eastern shore contains extensive farmlands, and certain agricultural practices areas can produce run-off containing nitrates, phosphorous, or other environmentally harmful substances. Other land and water uses, such as shoreline stabilization, construction activities and channel dredging both in the immediate area and within the watershed, also impact the natural environment through habitat modification and loss of water clarity through increased sedimentation.

In response to these threats, the National Park Service, as well as other local environmental agencies and organizations, monitor water quality throughout the area on a routine basis. Using these and other data, a State of the Bays report was recently released providing a "snapshot" of conditions in the Maryland coastal bay system. The results indicate a wide range of problems in the system, and that considerable effort will be needed to maintain and, in some cases, restore water quality and aquatic resources to healthy conditions.