Winds of up to 145 kilometers per hour (90 miles per hour) were reported in some parts of the city, according to the Hong Kong Observatory, which also warned of the potential risks of flooding.
More than 180 flights to or from Hong Kong's airport were canceled, and bus, tram and ferry routes suspended.
The Observatory said Tuesday morning that Nida had "weakened into a severe tropical storm and is moving gradually to the inland areas of Guangdong."
The Observatory issued the year's first No. 8 warning signal, the third-most severe, on Monday evening.
Speaking to reporters, an Observatory spokeswoman warned Hong Kongers "not to let their guard down" as the storm moved across the city.
"Places which have been sheltered before will become more exposed to high winds," she said, adding that the potential for a higher warning signal could be raised "cannot be ruled out."
Gusts of up to 145 kilometers (90 miles) per hour were recorded at Ngong Ping on Lantau Island, near the airport, while outlying Cheng Chau island was lashed by sustained 78 kilometer-per hour winds.
The MTR, Hong Kong's subway, was only running a limited service, while most bus routes were suspended, and all ferry and tram services canceled.
"The authorities aren't taking any chances," said CNN's Ivan Watson. "Hong Kong is used to these kinds of typhoons, and much of the city will likely be closed today."
The Observatory's warning was downgraded to a No. 3 strong wind signal early Tuesday afternoon, as the storm weakened and moved northwest away from Hong Kong.
China on alert
As the storm proceeded across Hong Kong and makes landfall in southern China, many cities in the Pearl River Delta region were bracing for impact.
The China Meteorological Administration issued a typhoon red alert -- the highest level of warning -- on Monday, its first such alert of the year, with people in affected areas warned to stockpile up to three days worth of food.
China's State Oceanic Administration (SOA) also issued a red alert for ocean waves and storm tides, warning that waves of up to 11 meters high could be expected off the coast of Guangdong Province.
The SOA estimates that the sea level off the Pearl River estuary could rise up to 220 cm (7 feet), and warned of the risk of flooding.
Shenzhen airport canceled all flights from midnight Monday through Tuesday morning, while farther north in Guangzhou more than 600 high-speed train runs were suspended, according to state-run news agency Xinhua.
As of Tuesday morning, Nida had been downgraded to a tropical storm, but alerts remained in place.
The China Meteorological Administration (CMA) said in a statement that Nida was expected to move to the northwest at a speed of about 25 kilometers per hour.
"The typhoon will land in Guangxi province at dusk today and it will weaken and be categorized of tropical low pressure at night," the CMA said.
Nida, also called Tropical Storm Carina, hit the Philippines on Saturday, pouring up to 11 inches of rain over the northern parts.
Northern Luzon and the provinces of Zambales and Bataan were on alert for flash floods and landslides triggered by the rains, the Philippine Atmospheric Geophysical and Astronomical Services Administration said.