The task facing the thousands of rescue workers, volunteers and soldiers was immense, with dozens of towns and villages devastated by the region's worst natural disaster in living memory.
Several thousand buildings were wrecked as the river Sava and its tributaries became a raging torrent and burst their banks last week, and many of those that remain will have to be destroyed.
"Houses built 20 to 30 years ago can be dried and renovated but for older ones it might be easier to tear them down and build new ones," Croatian Construction Minister Anka Mrak-Taritas said.
"All the floods that hit Croatia in recent history lasted for a shorter period. The water came and went... The longer the water stays the more problems we have when it recedes," she said.
In places where the floodwaters have receded they have left buildings and streets plastered with mud and littered with debris including everything from bashed-up cars to bloated drowned cows.
Complicating the clean-up operation in Bosnia was the possibility that some of the more than 120,000 landmines still littering the country 20 years after the war may have been dislodged.
The devices, which explode on touch, indiscriminantly killing or maiming anything in the vicinity, were often buried on the banks of rivers as demarcation lines during the 1992-5 conflict.
One such device exploded late Tuesday, causing no injuries. De-mining experts from the region were due to meet in Spacva, Croatia on Friday, the Bosnian news agency BHMAC reported, to work out an action plan.
- Lorries of rubbish -
Vast areas still remain under water, and tens of thousands of the nearly 150,000 people evacuated in Bosnia, Serbia and Croatia were stuck in shelters, unable to return home.
Those that have, if their homes are still standing, were taking appliances and other belongings out into the sun to dry, but much of it is sodden and will have to be thrown away.
In the northern Bosnian town of Doboj, where nine people died, 80 lorries full of rubbish have already been collected, some of it then deposited as temporary sites because the municipal tip was full, said Momcilo Zec, coordinating the operation.
Authorities in the area were also struggling to cope with the thousands of animal carcasses, too much for Bosnia's two incinerators, meaning some are being transported to Serbia in stinking lorries.
"The animals have to be incinerated within 72 hours to prevent disease contagion," said veterinary expert Edin Satrovic. Burying large numbers runs the risk of contaminating the soil, he said.
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