Work is underway on removing silt from areas of the Steeping River and Wainfleet Relief Channel, reports Environment Agency.
Under the plan, the dredging operations will remove sediment from targeted locations across 5.5km of waterway.
The stretch includes 5km of river between Thorpe Culvert and Dovecotes Farm, and 650m of the eastern end of the relief channel.
This first phase of dredging will last several months, to be followed by a second stage next autumn.
Findings showed that overall levels of sediment had reduced by 20% since the last investigation – but that more had accumulated in certain isolated pockets.
However, the dredging work will tackle those pockets, across which silt is an average of 43cm higher than desired.
Also, the plan includes options to improve the flow of water and further strengthen and maintain defenses.