Service has been restored on the Port Jefferson/Huntingon and Ronkonkoma branches after an earlier weather-related suspension, the Long Island Rail Road said.
Service is now operating with 30-45 minute delays in both directions.
Limited service has been restored on the Far Rockaway branch, being supplemented by bus service. Shuttle buses are running between Valley Stream and Far Rockaway due to a disabled train east of the Valley Stream station.
The Port Washington branch reported 10- to 15-minute delays in both directions because of water on the tracks.
The Oyster Bay branch had 90-minute to 2-hour delays because of downed trees blocking a track. Service later returned to normal.