The midweek nor’easter may have only blanketed the Big Apple with about 3 inches of sloppy snow, but it battered much of the tristate area — triggering a Thursday morning transit nightmare.

The Metro-North Railroad was operating on a reduced schedule with the New Canaan and Danbury branches suspended until further notice as a result of the storm — the second nor’easter to hit the region within a week.

“Expect extremely crowded conditions and delays due to the residual effects of the storm,” Metro-North warned riders via Twitter early Thursday.

The nor’easter Wednesday dumped about 2 feet or more of snow in parts of upstate New York, New Jersey and Connecticut.

New Jersey Transit rail commuters were also facing delays on some lines due to signal problems and downed trees across the tracks.

The transit agency said it was operating limited rail service Thursday “due to the significant impacts across the system following yesterday’s storm.”

“Customers should expect significant crowding conditions and delays,” NJ Transit said, adding that the cross-honoring of tickets will remain in effect Thursday with NJ Transit rail, light rail, bus and private carrier buses, PATH at Newark, Hoboken and 33rd Street in Manhattan, and the NY Waterway from Hoboken Terminal.

NJ Transit crews “worked through the night with hundreds of trees down across the state to restore as much service as possible for [Thursday] morning’s commute, and they will continue to work around-the-clock until all service can ultimately resume,” the agency said.

The New Jersey State Police said they responded to 506 motor vehicle crashes and 939 “motorist aids” involving mechanical breakdown, spinouts and flat tires due to the weather.

There were a slew of service cancellations on Amtrak for Thursday and service between Penn Station and Boston was temporarily suspended until at least 10 a.m. “due to severe weather,” Amtrak said.

“We hope to safely restore service as weather conditions improve and we apologize for any inconvenience,” Amtrak tweeted.

Meanwhile, some unlucky commuters were left stranded in Grand Central early Thursday after the storm snarled area rail lines.

The Harlem, New Haven, and Hudson Metro-North lines were temporarily shut down due to fallen trees blocking the tracks, signal power problems and other unspecified “weather-related infrastructure issues.”