The bill goes to the Senate for consideration, where the veto also is expected to be overridden. If that happens, it will be the first override since Bush has been president.
Eighteen representatives were absent and did not vote.
When Bush vetoed the Water Resources Development Act last week, he said, the bill had no fiscal discipline. The measure would authorize projects that impact waterborne commerce on the nation's rivers and coasts, as well as authorize habitat restoration and environmental projects.
Rep. John Mica, R-Fla., calling himself a "staunch supporter" of fiscal responsibility, supported the effort to override Bush's veto.
"We are doing as good a job as we can" representing constituents, Mica said.
Eddie Bernice Johnson, D-Texas, said "it gives no one pleasure to override" any presidential veto, but "we simply must begin to address" funding the projects in the bill.