Fishery managers are calling for an end to dredging in Aberdeen Harbour.
They say a quarter of all tagged smolts, young salmon, were lost in the harbour last year when dredge boats were active.
Salmon numbers in many rivers have been experiencing long-term decline and millions is being spent trying to establish the reasons.
Aberdeen Harbour Board has insisted a link between mortality and dredging is “improbable and speculative”.
Scientists have been tracking young salmon and trout on the River Dee since 2016 by inserting radio devices into the fish while they are upstream.
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River director Dr Lorraine Hawkins said: “In the last five years we’ve seen lower catches on the River Dee.”
“We found quite a high loss rate in the river, in the order of 20% to 40% and last year, for the first time, we saw additional mortality of smolts in the harbour.”