The floodgates opened at Benmore Dam last week, after days of heavy rain in the headwaters of the Waitaki catchment.
Meridian has been spilling from the mid-Waitaki chain stations since early December, and Lake Pukaki from late on Sunday.
Environment Canterbury (Ecan) principal scientist Shirley Hayward said there had been more than 1m of rain in the headwaters of the Waitaki catchment between December 3 and 10.
“This extreme high-rainfall prolonged event has caused high river flows into the hydro lakes,” she said.
A significant amount of debris was in the Waitaki rivers and lakes, Ecan harbourmaster Gary Manch said.
Lakes Benmore, Aviemore, Ohau, Waitaki and Ruataniwha were all affected.
Submerged and floating logs were a hazard for recreational river and lake use and would remain so for several weeks, throughout the summer boating season.
On Wednesday, flow in the Waitaki River at Kurow was 990cumecs, and had been varying around that level for the previous few days.