Specialist teams had to drain a ‘river’ of water from across the main artery towards the Queensferry Crossing at Cramond resulting in hour long queues for much of the morning rush hour.
It also caused delays through Burnshot lights which has also been crippled by a breakdown on the inside lane close to the junction.
Congestion, partly caused by a raft of breakdowns, was causing widespread delays on the A720 City Bypass with Baberton and Dreghorn worst affected.
Severe flooding is also causing issues at Niddry Road and Peniel Place on the A89 closing the road.
Some drivers ignoring the warning signs are reportedly stuck.
M8 traffic into Edinburgh was also very slow towards Hermiston Gait and around Whitburn and Bathgate.
The A71 near Livingstonwas hit by floods at the Oakbank roundabout adding to the woes for drivers.
The Forth Road Bridge was closed to double decker buses, causing busier than normal traffic on the Queensferry Crossing that remained opened to drivers “with care”.
Trains were hammered too with delays on all routes via Bathgate between Edinburgh and Glasgow Queen Street. Services were reduced to a half hourly service
The problem was caused by flooding at Linlithgow forcing operators ScotRail to divert services along a different route.
Routes to Central were unaffected.
ScotRail said it was caused by “heavy rain”.
Police Scotland told motorists: “Please be aware we have significant surface water being reported in several areas just now due to ongoing heavy rain.
“Drive with care.”
The Scottish Environment protection Agency had four flood alerts and 29 flood warnings in place this morning across Scotland.
According to forecasters, rain will continue on and off for most of the day.