Environment Canterbury's acting science director Dr Tim Davie said it could take up to 30 years for Te Waihora/Lake Ellesmere to heal itself.
The lake was shut for recreational use a decade ago after new guidelines were released in December 2009 and put into effect in 2010.
Davie said cyanobacteria (also known as blue/green algae) was most likely always present in the lake.
"It's important not to call it an infection," he said.
He said what happened in the lake was due to what was happening in the catchment above it.
Local Environmental Advisor for the Ellesmere Sustainable Agriculture Incorporated (ESAI). Carey Barnett .said it was in everyone's best interests to improve the water quality.
She said farmers had a similar sense of connection to the land, and family values, as local iwi and other groups involved in the lake.
She said everyone within the group was passionate about creating positive outcomes on the ground.
"Farmers have the same values as everyone else, and it's in their best interest as business people… as well as their family values. They have the same desire to enjoy our waterways," Barnett said.
The ESAI was incorporated in 2009, and had been proactive for a long time about issues like livestock in waterways, an issue faced by other rural communities.
"There's very few situations left in our area where animals are in waterways." Barnett said.
She said there were quite a few factors that went into levels in the lake; it was astounding the effect faecal matter dropped from birds flying over the lake actually had on the lake, she said.
The ESAI was working with farmers to better improve practices around waterways, as well as general environmental issues, and also to put regulations into practice to see if they were appropriate, Barnett said.
She said 112 farmers paid an annual subscription to the group, and they had a constitution to represent farmers with respect to water issues between the Selwyn and Rakaia rivers, as far back as SH1 and out to the east coast.