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Silt lines the bank along one side of the Ropewalk in Sandwich as part of measures to prevent more fish from dying from a lack of oxygen.
The maintenance work aims to improve the water quality of the stream and is costing around £2,300.
It is being conducted by Dover District Council, the River Stour Inland Drainage Board (IDB) and the Environment Agency and should be completed this week.
A spokesman for DDC said: "The main dredging works are due to be completed this week but there will be follow up works once we have allowed the silt to drain.
"We will then revisit to spread the silt, remove litter and debris, and most likely seed the area."
It comes after photographs of lifeless fish floating among the algae were shared on social media last summer.
Fisherman Simon Harrison slammed Dover District Council for its lack of maintenance and demanding the authority take swift action.
He claimed that the fish were struggling to sustain themselves because of the conditions.
He even produced a five-page proposal on how to tackle the issue.
The Environment Agency investigated the problem and officers confirmed that the fish in the Delf Stream had died because of low oxygen levels resulting from rotting weeds and high volumes of silt.
DDC said the matter was in hand with works planned for early 2020.
Fish have not been removed from the water during the works following advice from The River Stour IDB who said it was not necessary.
However DDC says preventative measures have been put in place if needed, with Mid Kent Fisheries (MKF) on standby.
MKF were also due to attend the site to monitor fish health and water oxygen levels.
A spokesman for DDC added: "The works are being undertaken from Sandwich Town Council land, who have given us permission to deposit the silt on their land.
"The paddock is secured and therefore out of bounds to general access.
"The area will be maintained in collaboration with Sandwich Town Council to retain access for future maintenance works."
Other maintenance include a range of tree works, and work to clear the embankment and surrounding vegetation.
DDC will also be contributing towards additional tree planting on the town council land.