The Observatory raised the T8 signal and the amber rainstorm warnings at 5:10am as Typhoon Pakhar approaches Hong Kong.
The typhoon is about 120 km southwest of Hong Kong and forecast to land west of the Pearl River Estuary at 12 noon.
Low-lying areas face possible flooding, the Observatory warns.
Cathay Pacific says it expects delays and cancellations on services on Sunday and Monday.
The MTR will run limited services on the Tung Chung and other lines.