Fresh water scientist Dr Marc Schallenberg, a research fellow at the Otago University, has been studying Lake Hayes since 1995 and believes the key to reducing algal bloom is to increase the number of daphnia - commonly known as the water flea.
Dr Schallenberg has recently begun a three-year study, which involves monthly testing of the lake and which is endorsed by the Friends of Lake Hayes association.
Because of its sediment makeup, the top layer of water in Lake Hayes heats up during summer, while the bottom layer remains the same temperature as it is during winter.
The warm layer prevents oxygen filtering down to the bottom layer and it subsequently becomes anoxic - meaning without oxygen - causing a chemical reaction which releases phosphorus and ammonia.
Lakes Wakatipu and Moke do not have this issue. During summer the bottom layer got higher and higher in nutrients, then in winter the two layers combined and ''you suddenly get a huge pulse'' of phosphorus and nitrogen, encouraging algae to multiply.
A study by Niwa in 2010, failed to find a way to reduce algae levels because the lake suddenly cleared up.
Dr Schallenberg hypothesised water fleas, in large concentrations, filtered the smaller algae in the lake and also had an indirect effect on larger algae.
''There's nothing else we can point to ... It was unprecedented how clear it was.''
''At the time we were thinking that if it is the daphnia that is clearing the lake, it will probably only last for a year or two. I speculated at the time that if the daphnia were the cause we would then have lots of little fish because they would be feeding on the daphnia.
''This number of daphnia coming in has unbalanced the lake in a favourable way.''
If the daphnia were proven to cut algae levels, allowing the flea to flourish would result in a clear lake, he said.
This could be done by decreasing the number of smaller fish by either netting them or introducing large fish to feed on the smaller ones.
At present, Lake Hayes has little or no daphnia and ''the algae problem'' is returning.
''I think this lake is a jewel of this area ... It's important that we have it clean because people fly over it and at the moment it's brown and that's not a good look.''
Dr Schallenberg is confident the study will determine how best to deal with the algae and Niwa is also looking at other methods to bind the phosphorus.
''We're talking about really complex food webs, where if you change one thing the repercussions echo throughout the whole system. ... But I think we have some pretty good leads about how to improve the lake.''
