Jablanica, some 70 kilometres (43 miles) southwest of the capital Sarajevo, appeared to bear the brunt of the downpours, which severed it from the rest of the country.
"It was terrifying, absolutely terrifying", a resident of the village of Donja Jablanica, Emir Arfadzan, told AFP.
"Boulders several cubic metres in size and thousands of tons of debris poured into our village. About 10 houses were destroyed, and there are casualties", said the visibly upset 62-year old man.
Photos on local media from the Jablanica region showed mudslides coming up to roofs of houses and a mosque with only its minaret sticking out.
A photo, published by regional railways authorities, showed a 200-metre (656-foot) section of a railway track suspended in mid-air after water triggered a massive landslide.
"People had no time... They only had seconds to save themselves. But we managed to save one child," Arfadzan said.
Police spokesman Ljudevit Maric told AFP that 16 people had lost their lives in the Jablanica region, according to data gathered by Friday afternoon.
BHRT national broadcaster reported that two more people died in the region of Fojnica, but this could not be confirmed with the authorities immediately.
The government of the Muslim-Croat Federation -- that along with the Serbs' Republika Srpska makes up Bosnia since its 1990s war -- has declared a state of natural disaster and formed a crisis headquarters.
Bosnia's tripartite presidency deployed the army to the flood-affected region.
"Engineering and rescue units as well as a helicopter from the Bosnia and Herzegovina's armed forces were urgently engaged to provide urgent assistance to civil authorities in responding to a natural disaster", the presidency said.
Jablanica, with a population of around 4,000, was initially cut off, but on Friday army and civil protection units arrived with heavy machinery to clear the mudslides.
However, like Arfadzan, many will not be able to return to their homes.
"They've marked our house with an X, which means we have to leave," Arfadzan said, adding that he will go to nearby Konjic, where his son lives.
A number of people from the area were reported missing, the authorities said, while some of the injured were evacuated with a helicopter from the European Union peacekeeping force EUFOR.
- 'Apocalyptic scenes' -
In Kiseljak, some 20 kilometres west of Sarajevo, houses, gardens and cars were under water, an AFP journalist reported.
The rain started on Thursday around 9:00 pm (1900 GMT) and continued all night, Kiseljak mayor Mladen Misuric Ramljak told AFP.
"Everything was normal until around 5:00 am when huge quantities of water poured. We certainly have several hundred houses flooded," he said, describing what he called a "biblical flood".
"These are apocalyptic scenes", the head of the nearby Kresevo municipality, Renato Pejak, echoed.
"Even the oldest residents don't remember so much rain falling in such a short time, that small streams turn into big rivers" and wash away bridges, he told reporters.
A large part of Bosnia's population is at risk due to heavy floods and landslides, the federal civil protection administration said in a statement earlier Friday.
The army, firefighters, police and utility companies were working in the affected areas.
In neighbouring Croatia, weather authorities issued a warning for the northern Adriatic coast, Istria peninsula and central part of the country due to the heavy rains.
It said urban flooding and interruption of traffic, communications, electricity and water supply were expected.
In the spring of 2014, the Balkans region was hit by its worst floods in more than a century, which affected 1.6 million people and left 47 people dead in Serbia and Bosnia.
Scientists warn that climate change is making extreme weather events more frequent.
Torrential rains and strong winds led to widespread flooding in central and eastern Europe last month, killing at least 24 people and devastating towns and villages.
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