Armed police showed up early in the morning, and more than 1,600 residents were hastily evacuated.
When it was safe, a dyke separating the two lakes was blown up in central China's Hubei province yesterday.
The 3.7km-long embankment separating Liangzi Lake and Niushan Lake was destroyed to help disperse surging floodwater, effectively merging the two lakes into one with a total surface area of about 370 sq km.
Among those who were evacuated were 261 employees - and their family members - of the Niushan Lake aquatic farm, which disappeared after the operation.
Hubei has been among the regions worst hit by the recent deadly downpours in China.
Due to persistent rain since last month, the water level of Liangzi, the province's second-largest lake, is more than a metre higher than that of Niushan, which is located on the other side of the dyke in the south-eastern suburbs of Wuhan city.
By 8am on Tuesday, Liangzi's water level had risen to 21.48m, 12cm above the safe level and 5cm higher than the last record high.
Heavy rain is forecast in Hubei up to Monday, and it is expected to raise Liangzi's water level to 22.38m.