The Otago Regional Council says heavy rainfall is expected in the headwaters of the Lake Wakatipu catchment over the next 24 hours, but towns are not at risk.
It said low-lying parts of the lakeside communities of Glenorchy, Queenstown and Kingston were unlikely to be affected, based on current forecasts and modelling.
But nearby Lake Wanaka is expected to rise close to a level that could cause surface flooding.
The council's director of hazards, engineering and science, Gavin Palmer, is urging everyone in low-lying areas to be prepared in case the rain is heavier than forecast.
The lakes are expected to be high from late today or early tomorrow and to stay high for the rest of the week.