Flooded areas included the Major Deegan Expressway, just south of the Cross Bronx Expressway, in the High Bridge section of the Bronx.
The flooding on the expressway started at around 1 a.m. Tuesday.
By 3 a.m. crews had to close all southbound lanes.
They remained closed for more than five hours as DEP crews responded and worked to alleviate the flooding by clearing storm drains.
Video from the scene showed a number of stranded vehicles on the highway. At least one had to be towed.
The northbound lanes were passable, but the right lane was flooded for several hours.
As the rain stopped, the water started to recede.
All lanes of the Deegan were finally back open by 9 a.m.
WATCH: Weather Or Not with Lee Goldberg - now available on our connected TV apps for Fire TV, Roku, Apple TV and Android
Weather or Not: When will spring shake off the chill? The AccuWeather outlook
MORE ACCUWEATHER RESOURCES
Check AccuTrack Radar
AccuTrack Radar New York City view
NWS Advisories, Watches and Warnings
School closings and delays
For weather updates wherever you go, please download the AccuWeather app.
Follow Lee Goldberg, Sam Champion, Brittany Bell, and Jeff Smith on social media.
Share your weather photos and videos, and Eyewitness News may show them on TV or any of our digital and social platforms