Water quality in the Maryland/Virginia Coastal Bays has been declining for many years from anthropogenic inputs, but conditions appear to have worsened abruptly following a shift from long-term dry to long-term wet conditions in the early 2000s. Annually and regionally averaged total nitrogen concentrations are approximately twofold higher, but ammonium (NH 4 +) concentrations are up to an order of magnitude higher than in the early 1990s. Averaged nitrate concentrations, however, changed to a lesser degree throughout the time course; water column concentrations remain very low. Total phosphorus has only increased in some bay segments, but increases in phosphate (PO 4 3−) have been more pervasive. There were differences in the year in which large increases in each nutrient were first noted: PO 4 3− in~2001-2002, followed by NH 4 +~a year later. The effects of a combination of steadily increasing anthropogenic nutrient increases from development, superimposed on nutrient loads from farming and animal operations, and groundwater inputs were accelerated by changes in freshwater flow and associated, negatively reinforcing, biogeochemical responses. Regionally, chlorophyll a concentrations have increased, and submersed aquatic vegetation has decreased. The system is now characterized by sustained summer picoplanktonic algal blooms, both brown tide and cyanobacteria. The retentive nature of this coastal lagoon combined with the reducing nature of the system will make these changes difficult to reverse if the current dual nutrient management practices are not accelerated.