The rain followed weeks of unseasonably warm weather. Temperatures are expected to drop at the weekend, with rain being succeeded by snow.
In the southwestern Serbian town of Novi Pazar, authorities declared emergency measures to cope with the overflowing Raska river.
RTS television said two men were carried away by the river while trying to protect their houses with wooden planks and plastic sheeting.
There was no official information about the incident. The RTS said a third man also fell into the river but was later pulled out.
In neighboring Montenegro, rescuers in the past two days have been searching for a 13-year-old boy who was dragged into the Adriatic Sea by a huge wave in the coastal town of Herceg Novi.
Heavy rain in northern Montenegro also caused rivers to reach critically high levels, while strong winds and waves lashed coastal areas.
In Bosnia, authorities said they are monitoring the situation after river levels rose considerably. Dozens of homes in the country have been flooded but no casualties have been reported.
“We expect the peak of the water wave during the day to be followed by stabilization,” said Bosnian hydrology official Majda Kovac.
Major floods in the region in 2014 claimed dozens of lives while submerging entire towns and villages.
