A bridge in Novi Sad was hit during the NATO air strikes
The Danube is to be declared safe for navigation on Thursday for the first time since 1999, when Nato bombed the bridges in the Yugoslav section of the river.
After a series of delays and complex negotiations, the Danube Commission, which oversees traffic on the river, confirmed that the central channel has been cleared of war debris and marked for safe navigation.
It also said that it has reached agreement with the Yugoslav authorities on lower fees and improved opening times for the existing pontoon bridge.
The logjam on Europe's longest waterway has hit shipping companies and river ports in all 11 Danube countries to the tune of $1m a day.
High costs
The European Union agreed to cover most of the cost of clearing the river, estimated at some $25m.
Until now, ship captains had to navigate at their own risk.
They also complained about the high fees levied by the Yugoslav authorities to open a pontoon bridge in the town of Novi Sad every weekend.
But Captain Danail Nedialkov, general director of the Danube Commission, said an agreement had been reached to gradually cut the fees and increase the opening times.
From 1 January the pontoon bridge will open twice a week, and from mid-March, three times a week, making it much easier for captains to plan their trips.
The pontoon bridge is to be removed in about two years' time, after the repair of the main bridge in Novi Sad.
Tenders for the clearance of debris and unexploded ordinance from the remainder of the Danube will also be published this week and officials expect the work to be completed by next autumn.
Despite the disruption, traffic through Novi Sad has steadily increased, reaching almost 500 ships this month.
But once the Danube is safely open for business again, that figure is expected to rise to 800 and more.