Developing: As Tropical Storm Irene heads north and the storm warning for the East Coast has been called off, officials have begun surveying the damage and what it means for Monday commute.
The Metro North railroad service said in a statement that it cannot with regular service Monday on any of its three lines, Hudson, Harlem and New Haven, citing significant damage to many portions of the system.
The Metro-North work crews will continue to inspect and repair the infrastructure throughout the night, Grand Central Terminal will open at 5:30 a.m. Monday.
The New Jersey Transit also has announced that it will not operate with regular service Monday due to damage to its systems, knocking out service on the Port Jervis and Pascack Valley lines.
New York Governor Andrew Cuomo announced that the Metropolitan Transportation Authority will begin restoration of service on the subway system at 6:00 a.m. Monday. The subways will run with limited exceptions, and officials say customers should expect longer waits and more crowded trains.
As of Sunday evening limited bus service was made available in New York City's five boroughs, and all MTA bridges and tunnels opened at 7 p.m.
The MTA also plans to restore near-normal service for Monday morning's rush hour on six of the Long Island Railroad branches, but advise customers to expect some cancelations and some trains operating with fewer cars than usual. The branches included are Babylon, Huntington, Ronkonkoma, Port Washington (with no service east of Great Neck), Hempstead, West Hempstead.
As of 8 p.m. Sunday Amtrak announced that most northeast regional services resumed between Washington and Philadelphia. All service between Boston and Philadelphia remains canceled.
Amtrak trains from New York to Florida will be canceled Monday, as well as the train between Lorton, Va., and Sanford, Fla.
Amtrak also canceled Acela Express service between Boston and Washington.
In Maryland officials warned commuters in the Baltimore-Washington area that they may encounter hurdles during their commute. The Maryland Transit Administration says there may be no parking-lot lights or working ticket machines at the Perryville, Aberdeen or Halethorpe MARC stations on the Penn Line due to power outages.
Officials say the Penn Line will operate on an "S" schedule.
The Massachusetts Bay Transportation Authority announced that most if not all modes of service will operate on a regular weekday schedule beginning Monday.
The Southeastern Pennsylvania Transportation Authority resumed bus and trolley service Sunday but regional rail service to the suburbs remained closed. Philadelphia International Airport reopened at 4 p.m. with limited arrivals but no departures.
A Greyhound spokeswoman said buses would begin to roll north out of Richmond Monday morning and hope to be running into New York by midday.
Officials say the three major New York City-area airports will resume most flights Monday morning after shutting down due to the storm over the weekend.
The Port Authority says John F. Kennedy International and Newark Liberty International airports will open to arriving flights at 6 a.m. Monday, with departures resuming at noon.
LaGuardia will follow and open at 7 a.m. Monday.
New Jersey's Teterboro suffered flooding and remains closed.
In Maine flights are expected to resume Monday at Bangor International Airport and Portland International Jetport, but it remains unclear when Amtrak's Downeaster will restore service between Portland and Boston.
Airlines had resumed flights Sunday at airports around Washington, Philadelphia and Richmond, Va.
Passengers are advised to call or check the websites of travel providers for the most updated information.
The Associated Press contributed to this report.