Heavy rains shut down LIRR service in and out of Penn Station and Brooklyn’s Atlantic Terminal on Monday during the evening rush, sending thousands of weary travelers onto the streets in Midtown Manhattan until service could be restored, transit officials and passengers said.

The “lightning, heavy rain and wind” that swept through the area all contributed to the widespread delays, MTA spokeswoman Nancy Gamerman said Monday night. Service was shut down about an hour earlier but delays began in the evening with switch problems near Jamaica, which crippled many of the Long Island Rail Roads branches.

MTA police temporarily closed access into Penn Station because of crowding in the terminal, Gamerman said. It reopened about 8 p.m., with rail service beginning minutes later. Service began out of Atlantic Terminal just after 7:50 p.m.

Systemwide delays persisted for hours after the shutdown, officials and passengers said.

The West End Concourse in Penn Station was shut down due to flooding and was reopened about 8:30 p.m., Gamerman said. Videos posted on Twitter show water gushing down from the ceiling in the Penn Station subway station and onto the tracks.

LIRR rider Jenny Lee, 58, a Ronkonkoma CPA who works in Manhattan, said she returned to work rather than wait in Penn Station or travel via subway, which she said has “too many people.”

But when she returned she couldn’t even get into Penn. Rather than riding her usual 5:41 p.m. train to Ronkonkoma, Lee was hoping to get on the 9:15 p.m. train. Leaning on a pole in Penn as she waited for the train, she said, “It’s always like that. Always delays.”

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Another rider, Chelsea Minella, 25, of Brentwood, who is an interior designer working in Flat Iron District, said she was hoping to catch the 6:53 p.m. train on the Ronkonkoma line to Brentwood but instead expected to get home a few hours late.

Like many of the other riders, she was kept out of Penn Station during the shutdown.

“They wouldn’t let us in,” she said, explaining she waited under an awning to keep dry. “This happens a lot. Delays. Suspensions. It’s aggravating. You get used to it. It’s no surprise.”

She summed up her frustrations: “We’re all trying to get home,” Minella said. “We’re all stuck in the same situation. There’s nothing you can do about it.”

Marilen Santos, 37, a claims processor hoping to catch the 6:42 p.m. train on the Port Washington branch to Bayside, decided to go have dinner rather than wait at Penn.

“I just want to get home,” she said, describing herself as “absolutely” frustrated with the situation.

“I don’t want to live on Long Island,” she said, because of the reliance on the LIRR.

She couldn’t comment more because she had to run to catch her delayed train.

By 9:45 p.m., the LIRR said trains were running close to on time.