"There are three victims of the floods," Prime Minister Boyko Borisov told journalists.
Parts of the region saw as much as 168 litres of rain per square metre over the past 12 hours, the national weather services said, with bad weather expected to continue throughout Wednesday.
A total of eight villages and Burgas's southern neighbourhoods were the most badly hit as heavy rainfall submerged roads, cut bridges and prompted electricity outages, local authorities said.
The rains also caused seven small dams in the region to overflow.
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