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Testing work for the Lower Thames Crossing has been phased to protect Benny the Beluga, who made the river his home in September.
Highways England had to carry out the investigations as part of the £6.8 billion pound project, which could remove 14 million vehicles from the Dartford Crossing every year.
Bosses altered the time allocated for their tests to ensure the whale was not disturbed, but say Benny is "very unlikely" to impact construction.
Benny was last spotted making his way back out to the Thames Estuary, experts from the British Diver Marine Life Rescue organisation said this week.
Gravesham council cancelled the town's firework display in November, in another attempt to keep the Arctic mammal safe.
A spokesman for Highways England said: "Benny the Beluga is not holding up progress on the Lower Thames Crossing.
The protection of wildlife and their habitats is an important priority for us.
"We phased our testing work to ensure we did not disturb Benny and that testing is now complete.
"He is very unlikely to have any impact on main construction as the tunnel entrances will be a fair distance away from the Thames itself."
Residents in Gravesend have embraced Benny's extended stay in the town, creating Christmas gifts to mark the whale's friendly visit.
Businesses across Gravesend have been coming up with different ways to celebrate his stay, including Benny's very own beer.
Christmas cards and fridge magnets are also on sale at Marie's Tea Room in the High Street, and knitted whales in Gravesend Borough Market.