It is 35 km (24 miles) long and rises in the Colzium Springs at Millstone Rig of the Pentland Hills. It travels through Harperrig Reservoir, past the ruins of Cairns Castle, through Balerno, Currie, Juniper Green, Colinton, Slateford, Longstone, Saughton, Balgreen, Roseburn and on to the nearest it gets to the city centre at the Dean Village, on the site of old watermills in a deep gorge. This ravine is dramatically spanned by the Dean Bridge, designed by Thomas Telford, which was built in 1832 for the road to Queensferry, and lies next to the New Town.
The river flows on past Stockbridge and Inverleith, Silvermills and Warriston. It then passes through shallows at a place known as Puddocky which is commonly thought to refer to "puddocks", the Scots language term for frogs, but actually took its name from the former Paddock Hall which was sited nearby. The river continues past Canonmills and Bonnington, the site of another watermill, to Leith where it widens into the old harbour and port at Shore Street. Leith Docks have been extended considerably out into the firth from the old shoreline, and there are now plans to discontinue their use as a port and use the area for housing redevelopment.
There is a Water of Leith Walkway beside the river for the 12.25 miles (19.6 kilometres) from Balerno to Leith, with approximately half a mile of the route on roads. The route forms an attractive haven for wildlife, passing through areas of woodland, often well separated from roads. For some distance the walkway follows the route of former railway tracks, and the remains of tunnels, bridges and other features of more than one railway may be seen at many places along the route.
A visitor centre is open to the public where the Union Canal passes over the Water of Leith via the Slateford Aqueduct at Longstone, in south-west Edinburgh. The Water of Leith Conservation Trust is dedicated to the conservation and enhancement of the river. The Trust provides education programs about the river and the environment.