An estimated 15,000 cubic metres of thick 'black ooze' sediment is expected to be removed from the Lower Vasse River, with a sediment removal program starting this month.
The 10-week project is co-funded by the City of Busselton and the state government, and is planned to improve the water quality of the river that flows through the centre of Busselton.
The Vasse River has experienced water quality problems during the summer months for many decades, and nearby residents have campaigned widely for action to improve the health of the waterway.
Sediment has accumulated in the river, creating up to a metre deep of what residents call 'black ooze' in some areas, which continues to drive algal blooms.
The sediment removal program is part of the Revitalising Geographe Waterways initiative under the state government's Healthy Estuaries WA program.
South West Region MP Jackie Jarvis said the Healthy Estuaries WA program would improve the Geographe catchment and other waterways across the South-West.
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"Addressing water quality in the Lower Vasse River is a focus for me as chair of the Vasse Taskforce," Ms Jarvis said.
"The Lower Vasse River is an important habitat for native freshwater fish, turtles, frogs and water birds."
In a video statement, City of Busselton senior sustainability officer Mathilde Breton said high levels of nutrients in the river had caused the water quality issues.
"Nutrients come from different activities, from the catchment, the fertilisers and manures we put on our farms and gardens, but also the sediment in the river releases nutrients when disturbed, or when there is low oxygen levels.
"Removing sediment, this is one source of nutrient we hope to reduce."
She explained that a small dredge will pump sediment through porous geotextile bags in Rotary Park, which will filter the sediment and return the water to the river.
She said the bags would be installed on a sand pad, covered in black plastic.
"We'll leave the bags for six to eight weeks, and after that time the sediment will be treated for acid sulphate, and taken offsite for reuse."
She said that for safety reasons, Rotary Park would be closed for three to four months, while the playground would be closed for up to seven weeks.
Stage one of the sediment removal project will focus on the 400m stretch of river between the causeway road bridge and the butter factory museum, with sediment to be removed up to the Busselton Bypass.
She said that coming stages of the project would treat the algal bloom in the river.
Local resident group, Voice of the Vasse River, has long campaigned for the City of Busselton and the Department of Water and Environmental Regulation to improve the health of the river.
Voice of the Vasse River spokesperson Jill Walsh said while the group was happy about the City's plans to dredge the river up to the bypass, it was disappointed the council intended to do the job in small stages over four years.
"Black algal mats are forming in different sections of the river all year round now," she said.
"We believe that it is far more urgent than that and needs to be done as soon as possible."