Many of the city's streets and highways are submerged under water.
New York City declared a state of emergency as strong torrential rains triggered flash floods, mud landslides and crippled movement across the city.
The National Weather Service reported that several areas received around 4 to 6 inches (10 to 15 cm) of rainfall since Friday morning, with an additional 2 inches expected in the hours ahead.
Governor Kathy Hochul declared a state of emergency across New York City, Long Island and the Hudson Valley as rains obstructed roads, crippled subways and other modes of transport.
The severity of the floods became evident when the New York Governor asked residents to plan their "escape routes" and not wait till water levels "crossed their knees".
Kathy Hochul urged all New Yorkers to check weather updates, schedules and exercise caution.
In a press conference, Governor Hochul stressed the importance of safety and cautioned against attempting to travel on flooded roads.
She also added that officials were worried about those in basement homes after a number of people drowned during Hurricane Ida in 2021.
The massive storm that hit the city on Thursday night left all of New York's burrows and surrounding areas with flood warnings.
Public Transport Halted
The city's public transport systems have broken down. Streets and highways are submerged under water.
"There are currently service disruptions on every single line in the NYC subway system amidst extreme rain and flash flooding across the city," said Manhattan Borough President Mark D. Levine.
New York city's subway systems have halted and at least one terminal of the LaGuardia Airport was closed on Friday.
The National Weather Service issued a stark advisory, urging residents to "move to higher ground now" and act quickly to ensure their safety.
The Subway department issued a statement warning the city's residents of limited train connectivity.
Photos and videos circulating the internet have revealed prominent parts of the city underwater. New Yorkers were seen wading through knee-high water.
Wettest Day In Two Years
In an online press conference, New York City emergency management commissioner Zachary Iscol said that Friday marked the wettest day since Hurricane Ida two years ago.
"That is not a statistic to take lightly. It highlights just how crucial it is for all of us to pay close attention to the weather advisories and to always take the necessary precautions," he added.
Mr Iscol also said that authorities expect another two to four inches likely throughout this afternoon.
"We have multiple contingency plans in place but ultimately, you know you're your first line of defense for yourself and your loved ones," he said.
Emergency alerts were sent to cellphones in the city at 9.30 am local time from the National Weather Service (NWS).