The project is designed to enable ships with a draught of 14.5 metres to enter Hamburg harbour – the limit is currently 13.5 metres. It is expected to cost around €385 million.
Tuesday's vote in favour from the state parliament of Lower Saxony meant that politicians hoping to see a boost to the north German region's economy have all their ducks in a row for the project which has been the subject of wrangling for years.
“The whole north German region will profit from this in the end,” Hamburg's mayor Olaf Scholz told the Hamburger Abendblatt newspaper.
But, as the Süddeutsche Zeitung daily reported, Friends of the Earth Germany (BUND) will make an emergency appeal to the Federal Administrative Court to stop the dredgers. They say there is enough evidence to show that the project would irreversibly damage the area's ecosystem.
“What we need now is more public involvement,” BUND spokesman Paul Schmid told the paper. Communities living on the riverbanks have not been taken into consideration, he added.
One of the main reasons for deepening the river is so that new cargo ships will be able to pass from the North Sea to Hamburg harbour.
The biggest ships, up to 350 metres long and 46 metres wide cannot yet be dealt with at the harbour, hindering its business.
Harbour managers say hundreds of thousands of jobs would be created if construction goes ahead, and warned of large losses otherwise.
EU gave the project the go-ahead last December despite protest from nature-protection groups. States which would be affected by the 136-kilometre stretch of water that will be deepened were asked to vote.
Schleswig-Holstein voted in favour immediately, but it has taken until now for Lower Saxony to make a decision.
The Green Party opposes the idea, and claimed that costs would likely rise once work starts, to around €630 million.