The flooding in Bosnia, Serbia and Montenegro is the worst in a century. Parts of Croatia have also been paralysed by the rising waters.
Spared the snow and ice gripping other areas of Europe, authorities said entire villages in Montenegro had been submerged by the flooding.
Serbian television reported some 300 homes homes and 1,400 residents were threatened in the areas of Vogan, Kasice and Stara Ljubovija.
According to the report, the Drina river - which runs along the Serbia-Bosnia border - was some 11 times higher than usual.
The Lim River also flooded some 50 houses and about 100 hectares (about 250 acres) of land in Prijepolje, the report said.
The city of Metkovic, in the Dalmatian region, on the Neretva river, has been hit hardest in Croatia, with around 700 houses in danger.
The Neretva has reached a height of 412 centimetres (162 inches), the highest in 50 years.
In the Lika region of Croatia, the cities of Kosinj and Gospic are also flooded, after the River Lika burst its banks, and the authorities declared a state of emergency there.
In Bosnia hundreds of people were evacuated after heavy rainfall caused severe flooding along the Drina River - the worst in 104 years.
But floodwaters there receded significantly overnight, leaving a trail of mud and debris in many areas on Friday.
Bosnian authorities had used rafts to rescue people on Thursday from apartments in Foca, and on the other side of the river, hundreds of people were evacuated in Serbia and Montenegro as the Drina flooded farms and roads.
Schools were closed, many people had no electricity or heat, and water supplies were contaminated along the river in all three countries.