Images from the city of Shaoguan, north of Guangzhou, showed residents on Wednesday making their way through flooded main roads, as water in some areas reached the tops of cars.
The muddy floodwater inundated shops and buildings, and people were seen clearing away the debris.
The low-lying Pearl River delta is home to the economic powerhouses of Guangzhou and Shenzhen, as well as several smaller but densely populated cities with major manufacturing and other industries.
Provincial emergency management authorities said earlier this week that direct economic losses were estimated at 1.7 billion yuan ($253 million).
Under the highest alert level, at-risk areas in Guangdong have been ordered to take all necessary measures including suspending work at factories and closing schools to minimise damage.
Other regions in southern China, including coastal Fujian province and Guangxi, have also been affected by record rains this month, forcing hundreds of thousands to evacuate.
Summer floods are common in parts of China, but these have been getting more extreme in recent years as a result of climate change.
Chinese authorities so far have not directly linked this year’s extreme floods to climate change.
Some local media have dubbed it a “once-in-a-century flood”, reporting that water levels have surpassed the highest recorded in 1931 and are approaching the area’s worst floods in 1915.