Track work started Monday morning and will continue through next year.
F service will be rerouted on the E line in both directions between Rockefeller Center and Jackson Heights-Roosevelt Avenue.
Weekday M service will be suspended between Rockefeller Center and Forest Hills-71st Avenue between 6 a.m. and 9 p.m.
The impacts to the F line mean it will be a lot more difficult for commuters to get on and off of Roosevelt Island.
Officials say 14,000 people live on Roosevelt Island and roughly three out of four take the F train on and off the island.
There is a tram, but it only carries 100 people at a time -- many of whom are tourists -- and with the track work, more people will cram onto the tram.
Residents like Jane Margaretten have been dreading the inconvenience for weeks.
"I'm tempted to take a six-month hotel stay in Manhattan, but I'm not going to do that. It's not feasible," she said.
The MTA is providing a shuttle train on the F line that will take riders off the island, but it only runs three times an hour and doesn't run overnight.
"We only have a shuttle train that starts in Queensbridge one stop away, comes to Roosevelt Island, and then goes to 63rd Street and Lexington Avenue at which time most of the people can use the Q train instead of the F train, the thing is the shuttle train only runs every 20 minutes, it ends at midnight, starts at 5 a.m., it's not like the usual subway service," said Judith Berdy with the Roosevelt Historical Society.
Transit officials say there was little choice. The rails that carried the F train between Midtown, Manhattan and Queens for the better part of four decades need to be ripped-up and replaced. That's nearly five miles of track.
"I frankly asked my team, 'Could we defer it? Could we do something differently? Could we, you know, find a different way to do it?' And the answer was an emphatic no," NYC Transit President Richard Davey said. "We really needed to get this track work done."
The MTA is covering the overnight hours with a shuttle bus that runs to Queens Plaza.
They say all the track work will improve overall reliability but it will take at least six months -- or maybe more.
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