Since September, MSc student and Fish & Game officer Helen Keeling has been spending one week a month carrying out water quality research on Lake Hayes and Lake Johnson.
Ms Keeling's one-year study is focused on their ongoing problems with algal blooms.
She has been awarded a University of Otago scholarship to find out if stocking or removing certain species and sizes of fish could increase the lakes' populations of the Daphnia water flea, which feeds on the algae.
Helped by Clutha Fisheries Trust field officer Aaron Horrell, she goes out on the lake once during the day and again after dark to take water samples, collect Daphnia and catch fish.
Reducing feeding pressure from fish, such as perch and bullies, could increase the density of Daphnia in the lake, which in turn could eliminate algal blooms, she said.
This method, along with a reduction in nutrient inflows, had been successful in restoring water quality in lakes in Europe.
Algal blooms affected lakes throughout the country, with blue-green algae producing toxins that threatened public health as well as affecting amenity and recreational values.
Both lakes had a "pretty serious'' problem with algal blooms, which were caused by decades of nutrient inflows from fertilisers.
Those inflows had reduced as a result of changes in land use and farming practices, but nutrients remaining in the lakes' sediment were released when the lake was "stirred up'' by winds.
"That's why, once a lake is nutrient-enriched, it's a very difficult problem to solve because you get this continued internal loading.''
Once she completed her field work next September, it would take up to a year to analyse her data and produce firm results.
It was possible they could form the basis of a trial in the coming years, either in an enclosure or using the entire lake.
