The MTA says there is now limited service on the Harlem, Hudson and New Haven lines following earlier suspensions.
Service was impacted as heavy rain brought flooding to areas across the tri-state region.
Officials urged commuters to stay home if possible. Those who must head out are urged to use extra caution and check the service status for your line before you go.
The MTA says it plans to have full service by the morning on the Hudson and Upper Harlem lines as severe storm damage cleanups continue overnight.