Construction machines worked to remove piles of rocks and debris covering the central town of Jablanica after the rainstorm early on Friday.
Huge quantities of rain fell in the area around Jablanica and nearby Konjic, causing sudden floods that broke into people's homes as they were sleeping.
Surging waters also triggered landslides that collapsed roads and hills, covering villages in mud and cutting off entire areas.
Bosnian media are reporting that rocks from a nearby quarry fell on the village of Donja Jablanica, burying houses.
Officials have said at least 16 people are confirmed dead, including a baby.
At least 10 are still missing while dozens are injured.
Rescuers sealed off Jablanica, banning any entry for outsiders while the search took place.
Some houses were submerged up to their roofs and as the water withdrew, rescuers could be seen walking over piles of rubble left behind.
Near the town of Konjic that was also hit by the storm, officials said some villages remained cut off on Saturday.
"Kilometres of roads no longer exist, nearly all bridges have been destroyed," Husein Hodzic from the local civil protection unit told regional N1 television.
"There is no electricity, all power poles have been swept away. There are no phone lines."
Bosnia's election authorities said local elections set for Sunday would be postponed in the flood-hit municipalities.
Human-caused climate change increases the intensity of rainfall because warm air holds more moisture.
This summer, the Balkans were also hit by long-lasting record temperatures, causing a drought.
Scientists said the dried-out land has hampered the absorption of floodwaters.
Flooding was also reported in Croatia and Montenegro in the previous days but caused less damage and no fatalities.
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