Rising as headstreams above Harperrig Reservoir in the Pentland Hills, the Water of Leith journeys northeast for 18 miles (29 km) through West Lothian and the City of Edinburgh before flowing into the Firth of Forth at Leith. Its catchment extends to 45 sq. miles (117 sq. km), of which approximately 70% is rural and 30% urban. The river has provided power for a succession of mills dating back to at least the 13th Century At their peak there were more than 70 and these included meal, corn and paper mills at Balerno, paper and snuff mills at Currie, a grain mill (which operated until 2001) and a paper mill at Juniper Green, a sawmill at Colinton and further mills at Stenhouse, Dean Village, Canonmills (where the river is known as the Puddocky Burn), Bonnington and Leith. These mills, along with sewage which entered the river, brought significant pollution, a problem which persisted into the 20th century.
The Water of Leith runs through steep post-glacial gorges at Colinton, Craiglockhart and Dean, which cut through sedimentary rocks of Lower Carboniferous age. The Water of Leith walkway was first recognised for its amenity value in 1949, but was not formally instituted until 1973. Today, it forms a picturesque and tranquil route for 13 miles (21 km) through the city.
The river has been historically managed by a group of Honorary Bailiffs, who can trace their origins back to 1605, although an active role has been taken by the Water of Leith Conservation Trust since its formation in 1988. Fishing is permitted by freely-available permits, and the river is stocked annually with brown trout by the City of Edinburgh Council. These are genetically-modified to ensure they do not interbreed with native fish.