The Canal and River Trust said there was one new boat in the capital every working day in the last year.
A spokesman said rising house and rent prices were driving people to chose houseboats as an alternative.
Over the last five years, the numbers have increased by 36% s to 2,964 boats in March 2014.
Boats without a home mooring are particularly increasing, with hotspots like Hackney seeing an 85% hike in just 12 months.
The increasing numbers, however, are squeezing the system with more and more people having to share the same space and facilities.
The trust looks after more than 100 miles of waterways across the capital including the Grand Union Canal, Regent's Canal and the River Lea navigation, but not the River Thames.
Jo Coggins, of the trust, said: "The boating community makes the waterways what they are but now there is more and more pressure on the system.
"Sheer economic factors are obvious and make buying or renting a boat in Zones 1 or 2 much cheaper than buying or renting a house or flat but people must remember the hidden costs."
Waterway licences, safety certificates, insurance and mooring fees are all additional costs for people living on canals and rivers.
Regular boat maintenance and planning supplies like water, fuel and toilet amenities are essential aspects of living on the water.
Boats without a permanent home mooring are only supposed to stay in one location for 14 days but not everyone adheres to the rules making it harder for others to find a free spot.
Alan Wildman, of the Residential Boat Owners Association, said the influx of people thinking the waterways were a cheaper way to live were starting to cause congestion.
"Canals are not housing estates on water, they are there for navigation," he said. "I'm not criticising people in London, but it's not like living in a flat on water."
"You have to keep water tanks full, batteries charged, toilets emptied. There's always something to be done."
A rise in the number of people choosing to live on canals in London is starting to put a strain on London's waterways, experts have said.