The Swan River Trust has started pumping nearly one tonne of oxygen into the Swan River every day in an attempt to keep plants and animals alive in a dying section of the river.

The pumping process is part of a plan to clean up and protect the health of the river system.

The oxygenation plant at Guildford Bridge was turned on this week for the first time this summer when oxygen levels were dangerously low.

Construction of a second oxygenation plant at Caversham Avenue will start later this year, with plans for other plants to be built along the river over the following years.

The cost of building and running the plant for the first two years will be nearly $1 million.

Low oxygen levels in the river are caused by a breakdown of organic matter on the river floor.

The matter comes, in part, from debris introduced into the river from the 660 drains that flow into the system.

Salt water, which is heavier than fresh water, exacerbates the low oxygen levels by acting as a barrier preventing oxygenated water from reaching the bottom of the river.

Trust environmental officer Suzanne Thompson said it was the first time the oxygenation technology had been used anywhere in the world in an estuary, and the Trust and the Department of Water were working to ensure that it was tested rigorously.

"Results from the Guildford and Caversham Avenue sites will be incorporated into a longer-term plan to keep oxygen levels in the Swan River suitable," Mrs Thompson said.

She said the Guildford oxygenation plant was still being tested, but results so far indicated that it could increase oxygen levels across more than 3km of the Swan River.

The plant costs up to $60,000 a year to run.

"By increasing oxygen levels, the health and amenity of the river will improve, providing a better habitat for fish and other aquatic life," she said.

Without the extra oxygen from the pumping system fish and other river life would die and the river would release an odour like rotten egg gas.

"If oxygen levels are left to get too low, they can spread throughout the entire water body and result in mortalities of oxygen-breathing organisms, including fish," Mrs Thompson said.

She said human impacts on the river, particularly the removal of water for drinking and irrigation and the addition of excessive nutrients and organic matter, had increased the need for oxygenation.

The process has been used successfully in the Canning River for more than a decade.