The Fleet arises on Hampstead Heath as two sources, which still flow on the surface as the Hampstead Ponds and the Highgate Ponds. Then they go underground, pass under Kentish Town, join in Camden Town, and flow onwards towards St Pancras Old Church, which was sited on the river’s banks. From there it passed in a sinuous course which is responsible for the unusual building line adjacent to King’s Cross station; the German Gymnasium faced the river banks, and the curve of the Great Northern Hotel follows the river which passes alongside it.

King’s Cross was originally named Battle Bridge, referring to an ancient bridge over the Fleet where Boudica’s army is said to have fought an important battle against the Romans; the name was changed in the 19th century, to refer to a statue of George IV, widely disliked, and quickly replaced by the lighthouse building that still stands today. From there, it heads down King’s Cross Road, from where the valley slope can still be seen in the surrounding streets, and into Clerkenwell; the comparatively steep valley is responsible for the Holborn Viaduct bridges which carry local roads over the valley floor.

The river then flows down Farringdon Road and Farringdon Street, where the valley broadens out, and straightens, and joins the Thames beneath Blackfriars Bridge.

The lower reaches of the river were known as the Holbourne (or Oldbourne), whence Holborn derived its name.

In Roman times, the Fleet was a major river, with its estuary possibly containing the oldest tidal mill in the world. In Anglo-Saxon times, the Fleet was still a substantial body of water, joining the Thames through a marshy tidal basin over 100 yards (91 m) wide at the mouth of the Fleet Valley. Many wells were built along its banks, and some on springs (Bagnigge Well, Clerkenwell) and St Bride’s Well, were reputed to have healing qualities; in the 13th century the river was called River of Wells. The small lane at the south-west end of New Bridge Street is called Watergate because it was the river entrance to Bridewell Palace.

As London grew, the river became increasingly a sewer. The area came to be characterised by poor-quality housing and prisons: Bridewell Palace itself was converted into a prison; Newgate, Fleet and Ludgate prisons were all built in that area. In 1728 Alexander Pope wrote in his Dunciad, "To where Fleet-ditch with disemboguing streams / Rolls the large tribute of dead dogs to Thames / The king of dykes! than whom no sluice of mud / with deeper sable blots the silver flood".

Following the Great Fire of London in 1666, Christopher Wren’s proposal for widening the river was rejected. Rather, the Fleet was converted into the New Canal, completed in 1680 under the supervision of Robert Hooke. Newcastle Close and Old Seacoal Lane (now just short alleyways off Farringdon Street) recall the wharves that used to line this canal, especially used by the coastal coal trade from the North East of England. (An adjacent narrow road, Seacoal Lane, also existed until the late 20th century when the present building fronting onto Farringdon Street was built, perhaps suggesting that a new wharf had been built near the old one.)

The upper canal, unpopular and unused, was from 1737 enclosed between Holborn and Ludgate Circus to form the "Fleet Market". The lower part, the section from Ludgate Circus to the Thames, had been covered by 1769 for the opening of the new Blackfriars Bridge and was consequently named "New Bridge Street".

The development of the Regent’s Canal and urban growth covered the river in King’s Cross and Camden from 1812. The Fleet Market was closed during the 1860s with the construction of Farringdon Road and Farringdon Street as a highway to the north and the Metropolitan Railway, while the final upper section of the river was covered when Hampstead was expanded in the 1870s.

The Fleet, or rather the sewer that now follows its route, can be heard through a grating in Ray Street, Clerkenwell in front of The Coach pub (formerly the Coach and Horses), just off Farringdon Road. The position of the river can still be seen in the surrounding streetscape with Ray Street and its continuation Warner Street lying in a valley where the river once flowed. It can also be heard through a grid in the centre of Charterhouse Street where it joins Farringdon Road (on the Smithfield side of the junction). In wet weather (when the sewer system is overloaded), and on a very low tide, the murky Fleet can be seen gushing into the Thames from the Thameswalk exit of Blackfriars station, immediately under Blackfriars Bridge.