The MTA is socking Rockaway drivers with thousands of dollars in fines for crossing a bridge that’s supposed to be free — even turning to collection agencies to recoup the cash, frustrated drivers say.

Peninsula residents get a free pass on the Cross Bay Bridge, but rather than just letting them motor through, the MTA charges their E-ZPass $1.41 and immediately refunds the same amount.

The problem is, drivers don’t always have the $1.41 in their accounts, so the MTA hits them with the full cost of the toll — $4.25 — plus a $100 fine for overdrawing their accounts.

To make matters worse, the agency has been letting those fines pile up for weeks before sending out a bill — which means some drivers aren’t even aware they’re overdrawn until they get a huge bill.

Rockaway resident Christina Calvache recently learned that she and her husband owe the authority an eye-popping $15,000 in fines and tolls accrued over just six weeks.

“It’s supposed to be free,” she said about the bridge. “[MTA] convinced me there was no way to waive the fees. I ended up paying them $500 because they threatened to revoke and take away my E-ZPass. I shouldn’t owe them anything and now they’re taking me to collections.”

Victims are paying the accrued tolls, because the MTA has threatened to take away their E-ZPasses if they don’t.

But they say the fines are a bridge too far — considering they aren’t supposed to be paying a dime for the crossing — and they’re fuming mad that the MTA won’t work with them to reduce the penalties.

“The state really has to fix this now,” said Rockaway resident Finbar Devine, 32, who is on the hook for nearly $11,000 thanks to the glitch.

It wasn’t a problem before cashless tolling was installed on the bridge, because a red light would illuminate to warn drivers their E-ZPasses were running low.

It’s the latest setback for a community that was devastated by Hurricane Sandy nearly six years ago. “It’s always something with Rockaway. We’re the lost neighborhood of New York City,” Calvache said.

A bill in the state legislature would cap fines at three times the toll amount and forgive penalties for those who pay the original toll. Rockaway Assemblywoman Stacey Pheffer Amato also wants to bar the MTA from siccing debt-collectors on drivers.

“Travelling under a tolling gantry with an underfunded E-ZPass account is a violation and can result in fees being assessed, this includes those Rockaway residents enrolled in the rebate program,” MTA spokesman Christopher McKniff said. “However, we work closely with all of our customers to resolve any issues or disputes.”