Transport links and water and power supplies in the city of 10 million are severely affected, and some residents are trapped in their homes.
Flooding has killed more than 180 people and caused chaos across China.
Police in neighbouring Anhui province even warned that alligators from a farm there had escaped due to the flooding.
Source: The Office of the State Flood Control and Drought Relief Headquarters, figures accurate as of 3 July
Wuhan's meteorological office released the red alert on Wednesday. It said to expect wind and rain, and flooding in both urban and rural areas.
Chinese media is reporting that more than 560mm (1.8ft) of rain has fallen over the past week, the heaviest ever in the history of the city, which is on the Yangtze River.
Roads and metro stations were inundated with water, and trains cancelled.
The last leg of the journey home for some people leaving Wuhan train station tonight is on foot, wading through the water.
A handful of couples passed me as I stood, almost up to my knees in it, at the traffic lights under the highway overpass by the railway station. A few coaches made it through the temporary pond, as did a few lorries. But there was no rush hour traffic in the worst hit suburbs tonight.
There is some respite; the rain has stopped for now. But as I write this there are still cars driving the wrong way down a highway slip road because the rain has blocked their route.
Water supplies have been cut off in some areas, and one residential district experienced a complete power black-out, according to local media.
Chinese Premier Li Keqiang is in Wuhan, the capital of Hubei province, to oversee relief and rescue operations.
Meanwhile, China's President Xi Jinping, has ordered the army to step up its relief efforts across the country.
Amid the crisis, official figures for the number of dead have fluctuated. On Wednesday state television put the overall toll at about 170.
Social media is awash with pictures of torrents of water thundering through metro stations, submerged cars and buildings, and firemen rescuing stranded people from across fast-flowing rivers that had previously been residential streets.
Police in Anhui shared a notice from Wuhu County's tourism bureau, which said that alligators had escaped from a farm due to the flooding. The notice said people were still trying to verify how many alligators had escaped.
It is not the only animal story to have grabbed the public's attention. On Tuesday a rescue team saved 6,000 pigs which had been stranded at their farm.
Photos of farmers emotionally bidding the animals farewell had been widely shared on social media.

The world's largest economy grew at an annualised rate of 3.2% in the three months to September, up from an earlier estimate of 2.9%.
The figure outstrips the second quarter growth rate of 1.4%, and was above economists' estimates of 3% growth.
The Commerce Department said the rate of growth was the strongest since the third quarter of 2014.
The strong growth may give further impetus to the Federal Reserve to raise US interest rates when it meets in the middle of next month.
A strong employment rate and steadily rising inflation may mean the the central bank is comfortable raising rates at the meeting on 13 and 14 December.
The Fed hiked its overnight benchmark interest rate last December for the first time in nearly a decade.
The GDP figure is a measure of the goods and services produced across the US economy.
The Commerce Department said: "The increase in real GDP in the third quarter primarily reflected positive contributions from personal consumption expenditures, exports, private inventory investment, and federal government spending, that were partly offset by negative contributions from residential fixed investment and state and local government spending."
It said consumer spending, which accounts for more than two-thirds of the US economy increased at a rate of 2.8%, compared with the initial estimate of 2.1%.
But business spending on equipment fell at a steeper 4.8% rate, instead of the previously reported 2.7%.
The Chinese city of Wuhan is on red alert for more heavy rainfall, after torrential downpours overnight left parts of the city submerged.
[NEXT_CONCEPT]
Strong consumer spending helped the US economy to grow faster than previously estimated in the third quarter.