The city issued a "red" alert, the first time the highest warning has been issued this year, for air traffic disruptions on Monday morning, Shenzhen Airport Group said late Monday.
Meanwhile, more than 60 flights have been delayed by over an hour.
Services at the airport have begun to resume when the alert was downgraded to "orange" at 5 pm Monday.
The Guangdong flood control authority announced that the rainy season began on Monday, much earlier than the April 15 forecast.
Heavy rain in Guangdong and neighboring Guangxi region over the past two days have seen water levels in some rivers and reservoirs rise to warning levels.
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