The River Dee, between Wirral and North Wales, is unusual in that comparatively little water occupies so large a basin. One theory of a contributory factor to the large basin is that once the River Mersey and/or the River Severn flowed into the Dee. A more recent theory, however, is that the estuary was not formed by water, but by ice being pushed southwards by the pressure of an icecap over the Irish Sea. The water has never been sufficient to scour out an adequate navigation channel through the deep glacial silt.

The Dee has always been an unpredictable river, with constantly shifting sediments, which affected the suitability of different anchorages from time to time. The river was however navigable as far as Chester for passenger and freight traffic up to the 17th century, when silt around Chester began to be a major problem. This however led to an increase in the fortunes of Neston and particularly Parkgate.

Man has probably contributed to the silting up of the River Dee. At one time the Dee Mills, owned by the earls of Chester, operated 11 waterwheels and also constructed a weir across the river at Chester, which reduced the tidal limit and the scour of the river. The river was frequently referred to as Chester Water.

Also, in 1737 a new canal, the New Cut, was completed at Chester, taking the course of the river five miles below Chester to the Welsh side rather than English side as before. The river then reverted to its old course at Parkgate, but gradually swung to the Welsh side all the way to the sea. This did however improve the situation in the short term, but land reclamation beside the cut at Chester further reduced the tidal scour and increased silting.

Parkgate, which was only an anchorage at the beginning of the 17th century, and also Holyhead, were both ports for shipping which mainly ran to Dublin. As there was a good road from London to Chester and a regular stagecoach service, passengers and their goods would travel to Chester and await good weather for their passage across the Irish Sea. They could no longer embark at Chester, but had the choice of two other routes. These were either by a short journey to Parkgate, followed by a long sea voyage or a much longer journey over land to Holyhead, followed by a shorter sea voyage. As the journey to Holyhead was over mountainous tracks unsuitable for wheeled vehicles, Parkgate developed as the most popular choice at that time. The passage to Dublin was very hazardous however. Ships were frequently wrecked, blown off course or attacked by pirates.

The depth of water limited the size of the ships using the River Dee, so trade remained mainly with Dublin. Liverpool, which had far greater depths of water in the River Mersey, built larger ships and thus developed trans-Atlantic trade. With the advent of steam power, larger ships could be built, ferries across the Mersey were more reliable and with the improvement in the transport system, Liverpool developed as a much more viable port. Parkgate, which by the mid-18th century was also a sea bathing resort, was further eclipsed by the development of New Brighton, which was more conveniently situated for the citizens of the prospering city of Liverpool. By the mid nineteenth century increasing silt had made the River Dee no longer viable for ferry services across to Wales or Ireland.

In modern times, the marshes and sandbanks of the River Dee provide an excellent site for birds. If weather conditions are favourable, the equinoctial spring tides reach the seawall in the Parkgate area on a couple of occasions a year, attracting birdwatchers from a wide area. For further information see Dee Estuary birdwatching.