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The lake is a popular holiday destination for hut holders and campers, but also recreational users such as day trampers, mountain bikers and fishers.
Water testing since late December showed high concentrations of Synechocystis, which could cause skin rashes, nausea, stomach cramps, tingling and numbness around the mouth and fingertips.
Despite the health warning windsurfers and kayakers were still seen using the water, although no health issues had been reported to Canterbury District Health Board.
Environment Canterbury councillor Ian Mackenzie said last week most had hoped that retiring over 90% of the lake’s catchment to conservation park from farming 13 years ago would have halted the decline and protected the lakes.
"It would appear that there may be multiple causes for the decline; from farming in the catchment to sewerage from the village, warmer winters, the effects of the floods up there 15 months ago, and legacy issues from back in time.
"It may even be that shutting up most of the catchment in conservation park has contributed in various ways to the problem."
A recent meeting involving a cross-section of the Ashburton community had recently gathered to identify what was causing the problems, and the community were working alongside the district and regional councils to find solutions.
An Environment Canterbury spokesperson said there had been much speculation about the cause but it was not always easy to establish.
"There are likely several sources of nutrients to the lake as well as other contributing factors.
"What we do know is that Lake Clearwater is enriched in nutrients; the Trophic Level Index (TLI) has been either mesotrophic (above three) or eurotrophic (above four) every year since 2006.
"Higher than usual levels of algal biomass were measured last summer, which have again been exceeded this summer."
The regional council was testing the water weekly for cyanobacteria in addition to their standard summer programme testing for E. coli. The warning would remain in place until two consecutive weekly tests were recorded at safe levels for contact recreation.
"Heavy rain can remove cyanobacteria from lakes, but can also contribute new nutrients for future cyanobacteria growth, so the recent heavy rain may or may not help resolve the problem."
The issue was also recurring at nearby Lake Emma, which degraded and became turbid and supertrophic around 2000. Despite reservation of the lake-edge land after 2000, it has not returned to a healthy state.
"Lake Emma appears to be trying to ‘flip’ between a turbid, green, phytoplankton-rich state and a clearer, aquatic plant-dominated state. Once degraded, lakes can take a lot of time to respond to decreased nutrient loading and other pressures."
The algae had potential to be transferred between lakes by lake users but liked nutrient-rich, warm, calm waters.
ECan has received numerous complaints about excessive growths of aquatic plants in Lake Clearwater, which had impacted on recreational uses like angling and boating and had become a health and safety issue.
Canterbury Medical Officer of Health Ramon Pink said the algal bloom could produce toxins harmful to humans and animals and contact with the water should be avoided until further notice.
Boiling the water did not remove the toxin.