Most of Long Island's groundwater is contained in three major aquifers. Precipitation is the only source of fresh water for this aquifer system. In general, the movement of groundwater is toward the north in the vicinity of the North Shore and toward the south along the South Shore. The presence of streams on the surface and aquicludes that impede flow within the aquifer add complexity to the flow pattern.

Groundwater may exit the aquifer system through subsurface flow into surrounding bodies of salt water, through entering streams that carry to water to the shore, or through uptake and transpiration by plants. Water also may evaporate from ponds. In addition, humans extract water from the ground through supply wells.

Most ponds, streams and wetlands on Long Island are actually surface expression of the groundwater. The surfaces of these bodies of water are the water table.

The subsurface of Long Island consists of three main aquifers. The shallowest is the Upper Glacial Aquifer, which consists of glacial till and outwash deposited during the Pleistocene ice advances. The largest of the aquifers, known as the Magothy, lies beneath the Upper Glacial. It is composed of Cretaceous deltaic sediments deposited about 80 million years ago. The Raritan Clay underlies the Magothy and restricts movement of water into the Lloyd Aquifer, which lies in contact with the bedrock. The Raritan Clay is an example of a confining layer.

In addition to these layers, Long Island contains numerous smaller aquifers and confining layers. The Gardiners Clay underlies the southern part of Long Island, where is restricts the movement of groundwater. A confining layer known as the Smithtown Clay occurs in the Towns of Smithtown and Huntington. The Jameco Aquifer is encountered beneath southern Brooklyn and Queens.