The package of improvements will be carried out in partnership with the Department of Transport (DoT) and South West Trains.
Work is due to get underway this month.
Plans include rebuilding the former Waterloo International Terminal, expanding platforms, new track and signalling, installing modern facilities and upgrading the power supply.
The investment is understood the be the biggest for decades and will deliver a 30% increase in peak-time capacity by 2019.
Improvements to depots and sidings will also help with the maintenance of the network's biggest ever fleet of trains.
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The station and infrastructure improvements are largely funded by the Department for Transport and as part of Network Rail's Railway Upgrade.
The works will be carried out by South West Trains' Network Rail Alliance of Skanska, Colas Rail, AECOM and Mott MacDonald.
Sir Peter Hendy, Chairman of Network Rail, said: "This is the biggest package of improvements for passengers travelling to and from Waterloo for decades. It will provide passengers with a better station, extra seats and new trains.
"As part of our Railway Upgrade Plan, Network Rail is investing £40 billion to provide a bigger, better, more reliable railway for passengers across Britain. The plans announced today will create a bigger, better Waterloo and improve passengers' journeys on our most congested part of Britain's railway.
"They are a long way from being the complete answer to the peak-time congestion on this packed commuter route, but they will make a big difference."
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(LM/MH)
