Local organisations and the Queenstown Lakes District Council are wanting more testing while admitting infrastructure could be a significant part of the problem.
One councillor said they had heard of anecdotal reports of tourists and freedom campers both bathing and toileting in the lake and its catchments.
The long-term water quality rating by Land Air Water Aotearoa (LAWA) has dropped from "excellent" to "good" in the lake and signals an increase in contamination over five years.
Over that time, the highest E.coli levels were recorded as 1046 E.coli per 100ml and the lowest as 1 per 100ml.
While the water is generally still safe to swim in, increased amounts of E. coli detected in tests can do serious harm, says Wai Wānaka’s research and science lead, Ben Youngman.
"E. coli is mainly representative of faecal bacteria, so it’s some form of animal faecal bacteria or you can get it from dead animals, human waste and things like that."
E. coli could cause serious harm to one’s health, especially concerning with Wānaka’s high tourist numbers.
"With E. coli comes a risk of camphylobacter infection, so there is a direct health impact as well."
Increased development across the area would most likely increase contamination if no adjustment was made to practices.
Queenstown Lakes deputy mayor Quentin Smith and councillor Barry Bruce could not give a definite cause of the change in quality, but noted infrastructure and waste management were crucial factors.
"The growth we've experienced in a relatively short period of time has created a whole lot of infrastructural demands," Mr Bruce said.
Mr Smith also said that waste management needed to be more of a focus in the region.
"We've got about $18 million over the next three years being invested in wastewater infrastructure, in the Upper Clutha alone."
Both councillors also commented on the impact of tourism with reports of freedom campers contaminating the lake.
"I hear anecdotal reports of people bathing in the lake and washing clothes in the lake. We have the freedom-camping issue where people are toileting in catchment areas," Mr Bruce said.
Mr Smith said that with restrictions in the freedom camping bylaws, it was difficult to manage freedom campers.
The poor water quality could also affect the ecology of the lake, with a subtle increase in invasive species across the lake being another indicator of worsening water conditions.
Wai Wānaka does quarterly water monitoring which they are looking to increase given the conditions.
They are also urging people to try and do their part by planting riparian buffers and using fewer chemical fertilisers.
That would help reduce overland water flow from contaminating the lake.
Lake Wānaka has at times had "no swimming" warnings during periods of heavy rain. This had been seen at both Lakes Hāwea and Wakatipu also.
