The Cypress Swamp of Sussex County, Delaware, is underlain by a body of late Pleistocene- to Holocene-age unconsolidated sediments. They form a mappable geologic unit named the Cypress Swamp Formation. Deposits of the formation can be found outside the current boundaries of the Cypress Swamp and record the erosion and redistribution of older Pleistocene coastal and Pliocene sedimentary units. The geologic and physiographic settings of the Cypress Swamp are similar to the Dismal Swamp of Virginia.

Deposition of the Cypress Swamp Formation occurred in environments ranging from fresh-water, cold-climate marsh and boreal forest, to fresh-water, temperate climate, forested swamp, and bog. About 22,000 years before present (yrs BP) organic matter began accumulating within the swamp. Silt, clay, and sand eroded from local dunes and surrounding uplands were transported into the Cypress Swamp, and redistributed by small streams and wind, and deposited in marsh, bog, and pond environments. Thin sheet sand deposits likely formed during storms or during seasonal thawing events. This environment persisted until at least about 14,000 yrs BP. In the modern landscape, sandy upland areas (>40 ft elevation) are likely the remnants of these older eolian dunes, stream channel deposits, and shallow pond shoreline deposits. Areas that are now swamp overlie former bogs, marshes, and ponds.

Over the past 10,000 years the climate has warmed, and temperate-forested swamp, bog, and floodplain environments have become more dominant. Erosional and depositional processes continued to level the landscape as organic-rich sediments were deposited in low-lying fresh water swamp, marsh, bog, and pond environments, and mineral-rich sediments were deposited closer to stream channels and along the fringes of higher areas. The construction of the existing network of ditches and roads, as well as timbering and log mining practices, have dramatically altered the environment of the Cypress Swamp.