The early "Big Game Hunters" vanished, but the coastal regions were resettled by peoples accustomed to village-style living ("tidewater communities") that subsisted on hunting and gathering marine shellfish, and eventually, on agriculture.

During the lowstand in sea level caused by the Wisconsin glacier, the Raritan River carved back into its headlands and captured the major drainages from the Newark Basin.

During warming at the end of the Pleistocene and Early Holocene, the area encompassing Raritan Bay changed from tundra to a landscape dominated by spruce and pine forests.

This rise in sea level has resulted in the landward migration of the shoreline (aided by storm-induced coastal erosion) as much as two miles in some portions of the coast since colonial times.

In the Keasbey, New Jersey area, large pits were dug to extract the clays for ceramics and bricks, and huge chemical dumps, fly ash piles, and landfills were created to accommodate the waste from the growing industrial empire.

The building of shore management structures (dikes, groins, seawalls), the spraying of DDT (and other pesticides) to control the mosquito problem, the carving of ditches to drain wetlands, the filling of shore lowlands, the channelization of creeks, highway and sewer construction, neighborhood development, and a myriad point and non-point sources of household, automobile, industrial chemicals, and ocean dumping all contributed to growing toxicity of the bay.

[citation needed] For most of the 20th century, the shores of Arthur Kill have been home to the largest petroleum importing, refining, and storage facilities on Earth; as a consequence the estuary has been host to major and minor oil spills.

[citation needed] The bay is a popular destination for recreational fishing due to its proximity to the densely populated areas of Central Jersey and New York City.