Hong Kong saw heavy rain overnight, with the Red Rainstorm Warning being issued at 1.30 am on Friday.
Parts of the northern New Territories were hit by flooding. So far, there have been no reports of any injuries.
The Observatory said heavy rain had affected the northern part of the New Territories – especially around San Tin and Ngau Tam Mei, and Sheung Shui – with 70 millimetres of rain falling in a single hour.
There were reports of flooding on Kwu Tung Road and Chau Tau Road in Lok Ma Chau, as well roads around Ping Che.
The thunderstorm warning was also issued as a south-west monsoon over the northern part of the South China Sea strengthened.
The Observatory warned of traffic congestion and disruption to normal school hours.