Cheshire's water resources have always been key to local sustenance and economic development; in recent years they have also proved a valuable asset for the leisure industry. In terms of size and importance, the two main waterways of the county are the Dee and the Mersey, fed by several smaller rivers, such as the Dane, Gowy, Dean and Bollin, and brooks, such as Todd Brook, Aldford Brook and Micker Brook.

The River Dee, which makes up part of the border with Wales, flows from Snowdonia to the Wirral Peninsula, passing through the city of Chester. Its fertile valley is known as auspicious for agriculture and its estuary is an optimal refuge for a variety of wild bird species. With regards to leisure, the river has long been a popular choice for water sports such as canoeing and rafting (although recent regulations have restricted this use). The River Mersey, which flows between Stockport and Liverpool Bay, passing through Warrington, is associated with the fairly prosperous Merseyside, as well as nature reserves (Chorlton Ees for instance), water sports and angling, which is very prevalent in the area.

Aside from rivers and lakes, the region uses a network of canals, most of them built during the initial phase of the Industrial Revolution with the main aim of transporting commodities. The Manchester Ship canal, which made up of navigable portions of the River Mersey and the River Irwell, continues to be used for heavy traffic. Nowadays, canals such as the Trent and Mersey, Rochdale and Peak Forest are also being successfully exploited for scenic tourism. In addition to other uses, fishing is fairly lucrative in Cheshire, with a number of natural bodies of water and artificial fisheries regularly preferred for this sport. Coarse angling seems to rank highest on list of holiday makers' preferences and is a hallmark of the region.