Both lakes were at normal levels for this time of the year and were not expected to rise significantly.
MetService has issued a heavy rain warning for Fiordland and southern Westland, and a severe gale warning for parts of Canterbury and Otago.
MetService meteorologist Daniel Corbett said the warm northwesterly flow to the east of the South Island and heavy rain to the west were caused by a front draped across the South Island.
Temperatures in the east were well into double figures today, with Oamaru recording a high of 16C and Timaru reaching 17C - well above the 10C average for this time of the year.
Mr Corbett said that was a marked difference from the same time last week, when temperatures barely reached 6C.
"We were sitting in the bone-chilling cold, so quite a difference that's of course leading to the snow melt.
"And when you're getting some moisture coming over the divide, getting into the headwaters, needless to say the rivers are flowing pretty well.''
Mr Corbett said an initial surge of heavy rain in the west had eased after more than 100mm fell in Fiordland this morning. A second surge of moisture would come through late tonight.
The South Island was also being battered by heavy winds, with gusts easily in excess of 100km/h in parts of Southland and Otago this morning.
"They've eased back slightly, it's still quite windy. But there's going to be another surge - you can imagine almost like an accordion tightening as each section of the front comes through.''
The severe weather warnings are excepted to remain in place until conditions ease tomorrow.
