In the 1970s, the Chesapeake Bay was found to contain one of the planets first identified marine dead zones, where waters were so depleted of oxygen that they were unable to support life, resulting in massive fish kills. In 2010 the bays dead zones were estimated to kill 75,000 tons of bottom-dwelling clams and worms each year, weakening the base of the estuary's food chain and robbing the blue crab in particular of a primary food source. Crabs are sometimes observed to amass on shore to escape pockets of oxygen-poor water, a behavior known as a "crab jubilee". Hypoxia results in part from large algal blooms, which are nourished by the runoff of residential, farm and industrial waste throughout the watershed. A 2010 report criticized Amish farmers in Pennsylvania for raising cows with inadequate controls on the manure that they generate. Farms in Lancaster County, Pennsylvania generate large quantities of manure that washes into tributaries of the bay.
The pollution entering the bay has multiple components that contribute to algal blooms, principally the nutrients phosphorus and nitrogen. The algae prevents sunlight from reaching the bottom of the bay while alive and deoxygenates the bays water when it dies and rots. Soil erosion and runoff of sediment into the bay, exacerbated by devegetation, construction and the prevalence of pavement in urban and suburban areas, also block vital sunlight. The resulting loss of aquatic vegetation has depleted the habitat for much of the bays animal life. Beds of eelgrass, the dominant variety in the southern Chesapeake Bay, have shrunk by more than half there since the early 1970s. Overharvesting, pollution, sedimentation and disease have turned much of the bay's bottom into a muddy wasteland.
The principal sources of nutrient pollution in the bay are surface runoff from farms, as well as runoff from urban and suburban areas. About half of the nutrient pollutant loads in the bay are generated by manure and poultry litter. Extensive use of lawn fertilizers and air pollution from motor vehicles and power plants are also significant nutrient sources.
One particularly harmful source of toxicity is Pfiesteria piscicida, which can affect both fish and humans. Pfiesteria caused a small regional panic in the late 1990s when a series of large blooms started killing large numbers of fish while giving swimmers mysterious rashes; nutrient runoff from chicken farms was blamed for the growth.