Human remains have been found in the Maribyrnong River after an arm was initially discovered floating upstream at Moonee Ponds in Melbourne's north.

The limb was found by walkers about 1:30pm along the river near the Boathouse restaurant, which is owned by celebrity chef Gary Mehigan.

Police and SES crews then began a search of the area and uncovered further remains about two kilometres from the initial discovery.

Crews are continuing to conduct line searches and homicide squad detectives have also arrived at the scene.

Police said they did not know how long the remains had been in the river and were treating it as suspicious.

Detective Senior Sergeant Stuart Bailey from Victoria Police said they had yet to identify what part of the body the other remains came from, but it appeared to be another limb.

"Both limbs have been taken to the Victorian Institute of Forensic Medicine, there will be pathology work done on them," he said.

"At this point we don't know who the person is... we've looked through missing persons records but there's nothing obvious to us."

He said the river was initially flowing upstream but had changed direction in the afternoon, so crews had widened the search in both directions.

One customer at the Boathouse restaurant, Nadia, said she and other patrons were shocked.

"We spoke to a few others who said there was an arm found, from the shoulder down to the wrist," she said.

"It looked like a male's arm. We come here every week, so it's a bit of a surprise.

"You come here for a coffee and they find something bad."