The Dutch and the Swedes were the first Europeans to have control of the region in the first quarter of the 17th century, but by the 1660s, the English were in complete control and more major alterations of the environment began at this time.

Founded in 1682 by William Penn, Philadelphia had approximately 5,000 inhabitants in 1700. The growth of agriculture was largely responsible for the transformation of the Delaware Estuary watershed from a wilderness to a pastoral landscape. Forests were cleared, resulting in erosion and the loss of topsoil. Shoreline dredging, diking, and filling resulted in the loss of tidal marsh and natural shoreline. Then, in 1799, the Estuary’s first official pollution survey noted contamination entering the river from ships, sewers and polluted wetlands.

By the 1840s, the deepwater ports of the Estuary had become manufacturing centers, and the railroad had transformed villages in South Jersey into regional centers for agriculture. By the end of the 19th century, increased population and industrialization had transformed much of the upper Estuary watershed. Fisheries were in decline, at least in part due to overfishing and pollution. Drinking water supplies were contaminated by pollution, primarily sewage, which caused outbreaks of typhoid and other diseases in urban areas. Both the industrialization and pollution of the water led to a dramatic decrease in the recreational use of the Delaware. It became less of a regional focal point as fewer people had, or wanted, direct contact with the water.

By the 1940s, the upper Estuary's fisheries were all but destroyed and water quality concerns were voiced. World War II overshadowed environmental concerns and more pollution flowed into the Delaware Estuary from defense-related industries. By 1950, the urban reach of the Delaware was one of the most polluted stretches of river in the world, with essentially zero dissolved oxygen in the water during the warmer months of the year.

Throughout the 1960s and 1970s, increased state, interstate, federal and public interest, along with the passing of the Clean Water Act in 1972, led to dramatic improvements in the Delaware Estuary’s water quality. By the end of the 1980s, over $1.5 billion in public money, along with billions from the private sector, had been spent in cleanup efforts.

The Delaware Estuary is cleaner than at any time during the last century, yet problems with fisheries, stormwater runoff, toxic substances, and habitat fragmentation still remain.