Rotokawau/Virginia Lake is a classic example of how a lake can be degraded by small and apparently innocuous changes in its catchment, a 2012 Niwa report says.
The lake has been having algal blooms since 2007, often in spring.
Making it really pristine would require more intervention and Niwa suggested extra measures.
Its report on the lake was included in Guidelines For Artificial Lakes, which was commissioned by the Ministry for Business, Innovation and Employment.
The report followed a $700,000 Whanganui District Council spend to clear the lake of algal blooms.
Suggestions included having fewer ducks and swans, and changing the surrounding park to evergreen native vegetation with riparian vegetation at the edges.
"We looked at those recommendations and what we could practically do, we did," Whanganui District Council senior stormwater engineer Kritzo Venter said.
Aerators added in former Mayor Michael Laws' time didn't work as intended. But four ultrasound units were installed. The sound waves destroy the air bubbles that keep cyanobacteria afloat, causing them to sink to deeper water and decay.
These prevent the most serious algal blooms, Venter said.
The council also changed the outflow from the lake. Instead of releasing surface water it releases the deeper, nutrient-rich water, and aerates it in the process. That water enters Whanganui's stormwater system and goes into the river near the Dublin St Bridge.
Divers at the lake check the ultrasound units and lake outlet monthly.
More aeration for the lake would make it harder for cyanobacteria to bloom, Niwa said.
The council could also have used chemicals to "cap" lake sediment and prevent the release of the nutrients that feed algae of all kinds, including cyanobacteria.
The lake was once an important eeling reserve for Māori. Now its water contains extra nitrogen and phosphorous from former septic tanks leaching into groundwater.
Other sources of those nutrients are decomposing leaves from the deciduous trees that surround it, faeces from birds and the decaying bread that people feed them.
It's a deep lake and below 6m the water is cold, still, full of nutrients and low in oxygen, the report says.
When it mixes with water at the surface, the nutrients, sunlight and warm temperatures feed a proliferation of cyanobacteria and other tiny organisms.
This proliferation can create the ammonia that sometimes kills birds and fish. It can also smell and look unpleasant.
Since Whanganui's stormwater and sewage were separated, there are no new septic tank nutrients entering the lake - but old ones could still be travelling in groundwater, Venter said.