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Fremantle coach Justin Longmuir believes captain Nat Fyfe's 2021 AFL season is almost certainly over after he re-injured his right shoulder against Sydney.

Fremantle captain Nat Fyfe's AFL season is almost certainly over after re-injuring his right shoulder in Sunday's 40-point loss to Sydney.

The two-time Brownlow Medallist fell awkwardly while contesting for the ball shortly before halftime at Metricon Stadium and didn't return for the second half.

Fyfe had pre-season surgery before dislocating the shoulder in a marking contest against the Western Bulldogs early last month.

The 29-year-old returned against Carlton earlier in July but after dislocating the joint for a second time, Dockers coach Justin Longmuir expects his superstar midfielder to have to go under the surgeon's knife again.

"It's the same injury he's had this year and been playing with so we'll have to look at what we do now," Longmuir said.

"Likelihood is he'll probably be going to surgery I'd imagine, now he's had a re-injure of it so his season might be done."

The Dockers also lost star forward Michael Walters in the third quarter to a hamstring injury.

Longmuir said that too looked serious and with just four games remaining, the 30-year-old's campaign could also be done and dusted.

The double-injury setback caps a horror year for the Dockers who lie 10th after their loss to the Swans and with their finals hopes hanging by a thread.

Key forward Matt Taberner (calf) and ruck Sean Darcy both played against the Swans, although Darcy looked very proppy on the left knee he injured against Geelong last weekend.

Meanwhile, midfielder Stephen Hill's return from a hamstring in the WAFL last Saturday ended when the 31-year-old suffered a recurrence of the injury midway through his comeback match.

It leaves Longmuir scrambling for bodies ahead of a clash with reigning premiers Richmond next weekend.