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Environment Canterbury says the mats develop and grow in flowing rivers but would not grow significantly on the bed or beaches of Lake Hood, which is partially fed from the river.
Ashburton zone lead Janine Holland said regular floods and freshes in the river usually scoured away algal growths.
‘‘However, this summer the Ashburton River has not had the floods and freshes that the bigger braided rivers have had.’’
Health warnings have been issued for the river at Hills Road, State Highway 1, Boundary Road and the river mouth.
Ms Holland said it was not uncommon in summer in rivers such as the Ashley and Opihi.
‘‘In the Ashburton, it means that a long period of stable summer low flows and high temperatures have allowed the cyanobacteria mats to develop and dominate the bed algal community.’’
People are being told to avoid the areas with health warnings and animals, particularly dogs, should not be allowed near the water until the warnings have been lifted.
The algae looks like dark brown to black mats and could produce toxins harmful to people and animals.
Exposure may cause skin rashes, nausea, stomach cramps, tingling and numbness around the mouth and fingertips.
Ms Holland said higher flows in the river in summer would lessen the degree of river solar heating and would result in lower concentrations of nutrients.
‘‘Both of these factors will lower the risk of widespread or persistent cyanobacteria mats.’’
ECan is currently reviewing 88 consents to take water from or adjacent to the river, with the aim of raising minimum flows. To date, 50 have been decided.
Consent holders were given new proposed conditions and encouraged to find alternative water sources.
One consent holder has proposed alternative conditions, which have been publicly notified and will be the subject of a hearing in April.
Six submitters have opposed the alternative conditions and one is in support; all wish to be heard at the hearing.
The Ashburton River has a north and south branch and tributaries include Taylor Stream and Pudding Hill Stream.
While the river provides habitat for birds, fish, plants and other species, it has also been a source of irrigation for farmers and land within the Ashburton water zone is considered among the most productive in the country. ECan is continuing to monitor sites along the river for the algal mats.