Salmon fishing groups have called for urgent action over the "unprecedented collapse" of a major run in Argyll.
The 2017 count from the River Awe in the south-west Highlands is projected to be the lowest since records began.
Fishery groups believe the declining salmon count is the result of "intensive" fish farming in the area, and the spread of sea lice at farms.
The government said a number of factors could be to blame, but said a project was under way to tackle the lice issue.
MSPs are set to hold an inquiry into the industry in early 2018, after the rural economy committee studied a petition from Salmon and Trout Conservation Scotland (STCS) about protecting wild fish from sea lice breeding in salmon farms.
'Run the gauntlet'
The group said this year's count from the Awe has only been running at a third of the 2016 count, which was itself only just above the all-time low since records began in 1965.
The 2016 total was 807 fish, but STCS said the 2017 count may "struggle to reach 400", with 30 weeks of the season already past.
They said juvenile salmon migrating from rivers in the south-west Highlands had to "run the gauntlet" close to lice-producing salmon farms the whole way up the west coast before reaching the open ocean.
STCS wants farms moved into closed containment tank systems to prevent the spread of parasites, saying only this could allow both farmed and wild fish to thrive.
Director Andrew Graham-Stewart said the numbers of mature west Highland sea trout had "collapsed" since the arrival of intensive fish farming, and said wild salmon numbers were also now in a decline which is "accelerating into a free fall".
Roger Brook, chairman of the Argyll District Salmon Fishery Board, said rivers like the Awe were facing "a very precarious future", and called on the government to make changes.
He said: "The Scottish government has promoted the continued expansion of the salmon aquaculture industry whilst refusing to implement adequate control on the siting of farms and the levels of sea lice on the farms.
"We call upon the Scottish government to insist that future farms are sited away from the probable migration routes. The worst existing farms, both in terms of location and lice control, should now be closed."
Scotland's farmed salmon industry continues to grow, with exports rising by 17% by value last year. However, there have been persistent concerns about sea lice, which can spread at farms and potentially damage ecosystems.
Efforts have been made to tackle the spread of lice at farms with "cleaner fish" which attack and eat the parasites. Scottish Sea Farms said their use has been "transformational", with lice levels at a three-year low at the end of 2016.
A spokeswoman for the Scottish government said: "We recognise that a number of factors may be having an impact on wild salmon stocks, including the activity of aquaculture, which can result in elevated numbers of sea lice in open water and hence is likely to increase the infestation potential on wild salmons.
"The magnitude of any such impact in relation to overall mortality levels is not known for Scotland. Marine Scotland Science has recently commenced a project to address this issue."