Maldives Meteorological Service has issued a white alert, warning of swell waves across the country over the next 24 hours.
It said there would be swell waves during high tides at around 5:00pm for northern atolls, 5:30 pm for central atolls and 7:00 pm for southern atolls on Sunday.
Heavy rains and thunderstorms are also expected in the southern atolls, with moderate showers in other regions.
The rough weather is caused by a low pressure trough formed over the country which is expected to move further south.
Floods were reported in many islands over the last two days.
Some 111 millimetres of rainfall was recorded in Addu city Gan, and 56 millimetres of rainfall was recorded in Gaaf Dhaal Kaadedhoo on Friday.
Swell waves caused flooding in Fuvahmulak on Saturday, causing some damage to vehicles and food carts.
The city’s mayor, Falah Shareef, said 15-foot waves struck the city although no damage was reported to households.
He said it was the first time in 30 years that such large swell waves had affected the atoll, which is considered one of the highest land points in the country.
According to the National Disaster Management Center, 22 islands and two cities have been affected by heavy rains and storm surges in the past week.