Many residents got their first clue when the parking spaces suddenly had numbers. It had always been free to park at the train station, even as a monthly ticket on the LIRR topped $375.
But officials blame residents and tourists from Fire Island who routinely dump their cars there. What's more, officials say the lot needs a series of expensive improvements, like security cameras.
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But of the 106 LIRR parking lots, 70 percent are either free or have at least some spaces that are free. That includes all of the lots on the Montauk branch and most lots on the Ronkonkoma, Babylon, Far Rockaway and Oyster Bay branches.
Just 30 percent of the rail road's lots require monthly permits or daily fees, which includes most of the lots on the Port Washington, Long Beach and West Hempstead branches.
Bay Shore's lot will join those, with 325 spots marked in red and reserved for residents for $90 a year.
Still, many say their commute is already expensive enough.
The parking fees are slated to take effect on January 4.