It rained overnight from Tuesday to Wednesday in the north-eastern city after five consecutive days without showers.
However, the Bangladesh Water Development Board has forecast moderate to heavy rain, lowering the risk of fresh flooding.
"Moderate to heavy rains will continue in the city this week," said Saeed Ahmed Chowdhury, a senior meteorologist at the Sylhet Met Office.
Many areas in Sylhet are still waterlogged, though the situation has improved in various parts of the city over the past few days.
The water level in the Surma has decreased over the last few days but it rose in the Kushiyara River, which flooded at least six upazilas in Sylhet.
Most of the areas in Sylhet, including five municipalities and 99 out of 105 unions in 13 upazilas have been flooded since Jun 15.
More than 2.1 million people from 16,966 families and 30,940 houses were affected by the floods, Sylhet Deputy Commissioner Mujibur Rahman said.
The authorities are distributing aid to the affected, he added.