The start of the Mersey is at the confluence of the River Tame and River Goyt in Stockport. It flows westwards through the suburban areas of south Manchester, then into the Manchester Ship Canal at Irlam, becoming a part of the canal and maintaining the canal's water levels. After 4 miles (6.4 km) the river exits the canal, flowing towards Warrington where the river widens. It then narrows as it passes between the towns of Runcorn and Widnes. From Runcorn the river widens into a large estuary, which is 3 miles (4.8 km) across at its widest point near Ellesmere Port. The course of the river then turns north as the estuary narrows between Liverpool and Birkenhead on the Wirral Peninsula to the west, and empties into Liverpool Bay. In total the river flows 70.33 miles (113 km).
A railway tunnel between Birkenhead and Liverpool as part of the Mersey Railway opened in 1886. Two road tunnels pass under the estuary from Liverpool: the Queensway Tunnel opened in 1934 connecting the city to Birkenhead, and the Kingsway Tunnel, opened in 1971, to Wallasey. A road bridge, completed in 1961 and later named the Silver Jubilee Bridge, crosses between Runcorn and Widnes, adjacent to the Runcorn Railway Bridge which opened in 1868. A second road bridge, the "Mersey Gateway", opened in October 2017, carrying a six-lane road connecting Runcorn's Central Expressway with Speke Road and Queensway in Widnes. The Mersey Ferry operates between Pier Head in Liverpool and Woodside in Birkenhead and Seacombe, and has become a tourist attraction offering cruises that provide an overview of the river and surrounding areas.
Water quality in the Mersey was severely affected by industrialisation, and in 1985, the Mersey Basin Campaign was established to improve water quality and encourage waterside regeneration. In 2009 it was announced that the river is "cleaner than at any time since the industrial revolution" and is "now considered one of the cleanest in the UK". The Mersey Valley Countryside Warden Service manages local nature reserves such as Chorlton Ees and Sale Water Park. The river gave its name to Merseybeat, developed by bands from Liverpool, notably the Beatles. In 1965 it was the subject of the top-ten hit single "Ferry Cross the Mersey" by Gerry and the Pacemakers.
Its name is derived from the Anglo-Saxon mǣres, "of a boundary" and ēa, "a river." The Mersey was possibly the border river between Mercia and Northumbria. Its Welsh name is Afon Merswy, and it has been given the alternative etymology of Celtic "môr-afon" meaning "sea river".
The Mersey is formed from three tributaries: the River Etherow, the River Goyt and the River Tame. The modern accepted start of the Mersey is at the confluence of the Tame and Goyt, in central Stockport, Greater Manchester. However, older definitions, and many older maps, place its start a few miles up the Goyt at Compstall; for example the 1911 Encyclopædia Britannica states "It is formed by the junction of the Goyt and the Etherow a short distance below Marple in Cheshire on the first-named stream." The 1784 John Stockdale map shows the River Mersey extending to Mottram, and forming the boundary between Cheshire and Derbyshire. In the west of Stockport it flows at the base of a cliff below the road called Brinksway before reaching flat country.