Democratic leaders in Congress promised a speedy override vote, The Hill reported. The measure passed by veto-proof margins.
The $23 billion water bill included $2 billion for the Everglades, The New York Times reported.
The Everglades project was agreed to in 2000. It had bipartisan support from the administration of President Bill Clinton and from Jeb Bush, President Bush's brother, who was then governor of Florida, as well as backing from Florida's two senators, Democrat Bob Graham and Republican Connie Mack.
The aim was to restore the flow of the River of Grass, a 70-mile wide slow-moving watercourse that carries water from Lake Okeechobee to Florida Bay. Reservoirs would have stored water during the rainy season to feed the Everglades and South Florida residents and farmers.
The project appears to have stalled. Graham and Mack have both left the Senate and the Bush administration is more concerned about terrorism and foreign policy, the Times said.
Biologists detail four new deep-sea 'killer sponges'
Pistorius testifies he didn't consciously pull trigger when he shot girlfriend