The Clutha District Council has issued a conserve water notice for both Tapanui and Milton after the flooding.
Clutha District Council service delivery group manager Jules Witt said the Tapanui Reservoir was 30% full and the Milton Reservoir was 40% full.
Mr Witt said the council had noticed a considerable amount of water use in those towns which had caused the low levels in the reservoirs.
"People wanted to get cleaned up so there were lots of hoses going and stuff."
The treatment plants were also struggling to produce the usual amount of water in addition to the excessive use.
Residents needed to limit their water use in these areas until the reservoirs caught up, Mr Witt said.
There was also a boil water notice in place for the Richardson North Rural Water Scheme and the Whitelea Rd area.
Mr Witt said several rivers were still dirty and the water treatment plants were struggling in the wake of the flooding.
"As long as water has been fully boiled in an electric jug any bacteria and viruses should be destroyed."
Mr Witt said the council was also monitoring other water schemes to determine if boil water notices should be implemented on them as well.
If water was boiled in a pot it should be left to boil for at least two minutes.
