Overall, water quality is degraded in the bays, worse in the streams, and best near the Ocean City Inlet (Isle of Wight and Sinepuxent Bays). Increased nitrogen loading into the Coastal Bays could induce a change from seagrass to macroalgae (seaweed) to phytoplankton (microscopic algae). Increasing signs of eutrophication indicate that the southern bays are close to, or have passed, a tipping point beyond which recovery will be difficult and lengthy.
Long-term trends in the southern bays indicate that improvements were made in water quality during the late 1980s/early 1990s. However, these trends reversed in the late 1990s, and currently water quality is degrading. Harmful algae blooms (especially brown tide), loss of seagrass, and reduced oxygen are problematic and anticipated to worsen if water quality trends do not change for the better.
Nutrient budgets indicate that groundwater (septic, shallow groundwater seepage, ditching), the atmosphere (including regional Mid-Atlantic sources), and surface runoff (agriculture) are significant sources of nitrogen to the Coastal Bays. Nitrogen in streams is related to the amount of agriculture in the watershed and streams may be the first areas to show improvement. It may take 15 or more years to see improvements due to the time lag of groundwater inputs. Phosphorus improvements may take longer if bay sediments are a significant source. Reduction of all nutrient sources will improve water quality.