The release of water was described by Meridian spokeswoman Claire Shaw as "very unusual" - the first time in 11 years it has been forced to do so at this time of the year.
Last night, flows in the river were expected to reach between 1800cumecs and 2000cumecs, close to six times its daily average of about 350cumecs.
New Zealand Transport Agency South Canterbury area manager Colin Hey said the 113-year-old wooden twin bridges closed between 6pm yesterday and 7am today for safety reasons.
The bridges would be checked today for damage.
The night closures would continue until the river was below 1500 cumecs.
The bridges were last closed in December 1995, when more than 3000cumecs caused major damage to some piers, which had to be replaced by new piles and the decking levelled.
Mr Hey said the last annual structural check found "significant decay" in some piers.
In the past 18 months, about $250,000 had been spent on them.
"Our consultants advise us they have about five years' life before we have to spend some major money - millions of dollars - to keep them going."
The two bridges were scheduled for replacement in 2014, but if there was "a catastrophic failure" that could be brought forward.
Yesterday, at 3.30pm, the Waitaki River at Kurow was flowing at 1415cumecs.
That was a result of more than 500mm of rain at Mt Cook over four days until yesterday, which over-filled the storage lakes of Tekapo and Pukaki, forcing Meridian to release water.
Miss Shaw said Meridian was using as much of the water as possible to generate electricity, depending on consumer demand, but was still having to spill excess.
"The worst of it appears to be over with rain easing, but at this stage we cannot say how long high flows will last. That depends on the inflows still to come."
At Omarama, parts of the town were flooded when the Omarama Stream rose from about 2cumecs to a peak of 55.5cumecs at 7.45am yesterday.
