Hundreds of dead fish have been found in Bushells Lagoon in north-western Sydney, leading Hawkesbury City Council to investigate the cause.

Richie Benson from the Hawkesbury Environment Network (HEN) has been monitoring the lagoon at Wilberforce, near Windsor, and was shocked to find hundreds of dead carp and eels there earlier this week.

His concern began in late December with reports of dead pelicans at Deep Lagoon, about half an hour north of Windsor, and later at Bushells Lagoon, which is extremely low.

Richie Benson says the fish are starting to stink. ( Facebook: Richie Benson )

"On Sunday I went out there to have a look at Bushells Lagoon and it seems that every carp and every eel in the lagoon is dead," Mr Benson said.

"I haven't seen one alive — fish or eel.

"It smells really bad, it's rotten, it's going make the water really poisonous in the next couple of days especially after today, a [40 degrees Celsius] day."

HEN said it was calling on the council to develop a water management plan to help preserve the natural value of the lagoon.

The council last night accepted a motion from Greens councillor Danielle Wheeler to urgently contact the NSW Environment Protection Authority about its investigation into the deaths of waterbirds, turtles, eels and fish in the Hawkesbury River Lagoons, which include Bushells Lagoon.

Dead pelicans have been found around Bushells Lagoon and will form part of the council's investigation. ( Facebook: Richie Benson )

The motion said the council would commission a report on how to better manage the area's lagoons and wetlands, develop a water management plan and carry out weed removal and revegetation programs with landcare groups and Wetland Warriors.

There is no official explanation for why the fish have died, but Mr Benson said he suspected it was a combination of hot weather and the low water level in the lagoon.

Mr Benson said while the drying out of the lagoon was part of the natural cycle, it was being accelerated by silt settling at the bottom.

Several dead turtles have also been found around the lagoon. ( Facebook: Richie Benson )

When he measured the temperature of the water last week, it was 34C.

"It's filling up with sediment quite quick, and because of that it's getting shallower," he said.

"The water's heating up quicker, then we're losing dissolved oxygen in the water.

"At that point there were some eels still alive, some of the smaller ones.

"The eels were actually getting out of the water and laying up on the mud to get air, but they end up drying out and dying."

Bushells Lagoon, in Wilberforce in Sydney's north west, is extremely low. ( Facebook: Richie Benson )

Cr Wheeler said she would be pushing the relevant organisations to make sure properties around the lagoon were abiding by regulations.

"Farmers still pump from Bushells Lagoon, even when it's as low as it is, so we need [Water NSW] to check that those licence conditions are being adhered to and that people aren't extracting water illegally," she said.

"We also need the people who are extracting water to be informed that that water now is likely to be heavily contaminated, so we're seeing some cyanobacterial blooms

"DPI, Water NSW need to be made aware of those as a matter of urgency and we need to contact anybody who's using any of the bodies of water that the water is now contaminated."

The general manager of Hawkesbury City Council, Peter Conroy, said the lagoon was ephemeral so it naturally dried out from time to time.

He said the council had gone back to Water NSW to get the details of water extraction licences, and to the EPA to find out what testing they will do.

"We're asking for them to confirm with us that they've undertaken an appropriate amount of testing and investigation ... that's to do with things that range from nutrients and water temperature through to perhaps the introduction of foreign materials to the water," Mr Conroy said.

"We want to know what's led to the death of, for example, the pelicans to make sure there's nothing we should be aware of and should be investigating."