Government water quality guidelines for recreational swimming areas are that those with less than 260 E. coli per 100ml ''should be safe'', whereas water with more than 550 E. coli per 100ml ''poses a health risk''.
Mr Olsen said it could be due to a number of factors including recent rainfall, cloud cover, water flow, bird activity, and stock in waterways.
It follows a case in Glenorchy last Friday when people were advised to boil water after the bacteria was detected in the township's water supply.
The Queenstown Lakes District Council issued a precautionary boil water notice to residents and businesses, saying about 180 households were affected.
''Advice from Public Health South is that all residents and businesses should boil water as a precaution,'' QLDC chief engineer Ulrich Glasner said last week.
The discovery came three days after the QLDC announced it would begin temporary chlorination of the water supplies in Arthurs Point, Luggate and Glenorchy, to ensure a safe drinking supply.