The estuary starts near Shotton after a five-mile (8 km) 'canalised' section and the river soon swells to be several miles wide forming the boundary between the Wirral Peninsula in north-west England and Flintshire in north-east Wales.

The estuary supports some important natural fisheries, including salmon and trout on their way to and from the freshwater river, as well as sea-fisheries and shell-fisheries, especially cockles.

From about the 14th century, Chester provided facilities for trade with Ireland, Spain, and Germany, and seagoing vessels would "lay to" in the Dee awaiting favourable winds and tides.

As the Dee started to silt up, harbouring facilities developed on the Wirral bank at Shotwick, Burton, Neston, Parkgate, Dawpool, and "Hoyle Lake" or Hoylake.

The estuary also plays a part in the most modern of industries as it provides the first stage of transport of Airbus A380 wings on their way to Toulouse via barge to Mostyn docks.