Canary Wharf was evacuated due to flooding, while westbound services weren't stopping at Mansion House and Victoria station also because of flooding. Bank was also closed due to overcrowding.
Trains are now stopping at Mansion House, though Circle and District lines aren't serving Victoria after a drain overflowed.
Canary Wharf has also reopened though the backlog has caused big queues.
There are also severe delays on the Bakerloo line due to an earlier faulty train at Waterloo.
It comes after Transport for London (TfL) said it was well-prepared for expected wintry weather.
The Met Office predicted snow will arrive in the South East this evening, and TfL said it was well-planned for the chillier temperatures and the prospect of snow.
It did warn of a "risk of icy conditions and some snow falling", but said it had 100,000 tonnes of salt stockpiled to see off any snow.
Today's weather: pic.twitter.com/y1NIpJxIhp— TfL Travel Alerts (@TfLTravelAlerts) January 12, 2017
Leon Daniels, managing director of surface transport at TfL, said there was "a well-rehearsed and thorough plan in place" to keep road and rail networks operating during snow and ice.
Airports across the capital have also cancelled a raft of flights - Heathrow and Gatwick slashed some ahead of snow earlier to day.
A 24-hour Tube strike caused the closure of many Zone 1 stations on Monday, with commuters forced to find alternative routes to work. Over 80 per cent more Santander bikes were hired on the day than the January average.