The provincial flood and disaster prevention department said on Sunday afternoon that floodwaters in the Bei River, a southern tributary of the Pearl River, were expected to peak at 37.3 metres (122 feet) by 1am, or about 5.8 metres above the warning line.
Warning levels had already been exceeded at 20 monitoring stations along the waterway by Saturday evening.
Northern and western Guangdong have been battered by intense rainstorms since Friday, breaking rainfall records for April in many places.
The cities of Qingyuan, Shaoguan, Huizhou and capital Guangzhou have been particularly hard hit, prompting flood alerts and rainstorm warnings for three days in a row.
According to the National Meteorological Centre, most of the affected areas have reported 200-350mm (7.9-13.8 inches) of rain since the start of the month.
By 8am Sunday, Shaoguan had registered 584.4mm for the month, well above the April record of 417mm set last year.
Dozens of hail and thunderstorm warnings were in effect across the province on the weekend, including orange alerts for Guangzhou, Dongguan, Yangjiang and Yangshan county in Qingyuan.
Orange is the second-highest alert level in China's four-tier rainstorm warning system.
More heavy rain is expected to fall across Guangdong - one of the country's most populous provinces - over the next three days, with northern Guangdong the most affected.
In central and northern Guangdong, northeastern Guangxi, and southern Jiangxi, cumulative rainfall for the month is forecast to reach 150-300mm, and surpass 400mm in some areas, according to the centre.
The provincial disaster prevention department urged its branches to "do their utmost" to ensure the safety of people's lives and property.
The Ministry of Water Resources in Beijing also sent three working groups to Guangdong on Sunday.
Officials were told to ensure there were systems in place covering monitoring and early warnings, flood control dispatch, flood diversion, patrol duty and emergency rescue.
Hundreds of people had to be evacuated from their homes in Qingyuan and Shaoguan, according to emergency services. No casualties were reported.
The wet weather also resulted in delays to dozens of flights at Baiyun International Airport in Guangzhou.
Richard Liang, who travelled through the affected areas on a high-speed train from Hunan province on Sunday morning, said the rainstorms appeared to have stopped in the main areas but the floods looked "terrible".
"It's not raining, but the sky is gloomy. From a distance, the Bei River has swollen and the water is muddy," he said.
"The water level of the rivers had risen, and the ground floors of buildings next to rivers and lakes were flooded. The buildings looked as if they were soaked in the water."
Cars were also damaged, trees brought down and farmland inundated.
It is the second major flood to hit the province this month. Thunderstorms hit southern parts of Guangzhou two weeks ago, the earliest start to the flood season since 1998, when records were first compiled.
More than 800 people had to be evacuated as waters rose then but there were no casualties.
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