The Western Australian Environment Minister has categorically ruled out banning agricultural fertilisers, despite figures showing nutrient loads in a critical water catchment have continued to exceed target levels for more than a decade.

The Ellen Brook runs through the Swan Valley and delivers 40 per cent of the nutrients flowing into the Swan River that contribute to algal blooms and fish kills.

Reducing that nutrient flow is seen as a vital part of the Government's effort to revive the river, but figures from the Swan River Trust show how difficult that task has proven.

A report on nutrient monitoring in the Ellen Brook from 2001 to 2013 showed short-term nitrogen level targets were achieved in only five years, and long-term targets were not achieved at all in that period.

The performance on phosphorous reduction levels was worse, with monitoring showing neither short nor long-term targets were achieved once in the 13-year period.

But WA Environment Minister Albert Jacob said although those figures revealed little or no progress, he would not agree to demands from Labor and environmentalists to ban river-harming agricultural fertilisers in the catchment.

"Agriculture is far too important an industry for this state," he said.

"They are growing our food. Cattle and a range of agricultural and horticultural uses sit in that catchment."

While political debate has focused on the issues of nutrients and fertiliser use, Mr Jacob said the problems and the solutions must be broader than that.

"No one of these programs is a single solution," he said.

"Oxygenation is a critical part of what has helped the river turn around since probably its lowest point in the mid-2000s."

The Swan River Trust has run programs in the past that pumped oxygen bubbles into the river, to try to prevent fish deaths.

Wetlands will only strip fraction of nutrients from clogged waterways

Mr Jacob said the Government was tackling the issue of nutrient inflow by installing nutrient-stripping wetlands, as well as infill sewerage programs.

The Government has spent $4 million creating a wetland along the Ellen Brook in order to remove nutrients from the waterway, which Mr Jacob said would have a positive effect.

He said the system would come online in winter.

It is estimated the wetlands will remove 660kg of nitrogen and phosphorous from a waterway that since 2001 has annually carried from five to 90 tonnes of nutrients into the river.

Mr Jacob conceded the 660kg yearly reduction, in percentage terms, was a small one.

Another nutrient-stripping project at the Eric Singleton reserve in the Perth suburb of Bayswater fares a little better, but still removes only a portion of the nutrients causing algal bloom and fish deaths.

"At Eric Singleton we get 50 per cent of our target. Ellen Brook is a lot smaller than that," he said.

When finished three years from now, the Eric Singleton reserve wetland will strip two of the 11 tonnes of nutrients the Bayswater Brook carries to the river.

Mr Jacob said there was no quick fix and that the effort to reduce the nutrient inflow will take decades because of the amount of nutrients already in the ground.

"The nutrient build up from historical land uses will still mean that 40 years of nutrient inflow coming into the river," he said.

"That flushing will still continue for another 40 years or so but these measures such as nutrient stripping wetlands, such as oxygenation, such as soil amendment products, a whole range of strategies are starting to make an improvement in the right direction."