The lakes include Wakatipu, Wānaka and Hāwea.
Earlier this week, the Otago Fish & Game Council issued a warning to anglers to be "extra cautious’’ of soft areas of silt, shingle and mud, especially around river and stream mouths.
And boaties were advised to be on the lookout for "new collision hazards’’ such as rocks, sandbars and — especially in Hāwea — submerged trees.
Lake Hāwea’s level is controlled by Clyde dam owner Contact Energy.
It is still half a metre above the minimum level allowed, but water barely reaches the bottom of the boat ramp, and the neighbouring popular swimming area is completely empty.
Contact dispatch trader Ashleigh Dumelow said yesterday Lake Hāwea had been lower than at present in 10 of the past 20 years.
"It has been a dry winter in the Clutha catchment, therefore the stored water in Lake Hāwea has been used to meet New Zealand’s electricity demand.
"We regularly have sustained low inflows as we experienced this winter, so this situation is not unusual.’’
She expected it would be unlikely for the lake to reach the minimum consented level.
"Spring rainfall events that typically occur from this time of year are relied upon to both raise lake levels and increase our generation capacity.’’
Lake Hāwea resident John Taylor said rainfall had amounted to just 26mm last month, 11mm in July and 39mm in June.
The water from Lake Hāwea represents 15% of the flow in the main stem of the Clutha River.
Lake Wānaka’s low level is most evident in Roys Bay, near the outlet of Bullock Creek.