Subway service on eleven train lines was running with “extensive delays” Monday morning and meteorologists warned flooding could further complicate the morning commute.

Trains on the A, C, E, B, D, F, M, N, Q, R and W lines were all running late, MTA officials said. One alert that went out just after 5:30 a.m. blamed some delays on “urgent track maintenance” needed in Brooklyn.

A subsequent alert just after 6:30 a.m. said further disruptions were triggered by a third rail power outage in Manhattan.

Straphangers took to Twitter to vent their frustrations.

Along with mechanical delays, the National Weather Service issued a flood advisory for parts of New York City and Northern New Jersey through 8:30 a.m., which could further complicate the morning commute.

Between half and one inch of rain had fallen and that much could continue to rain down, with the potential for minor flooding in Manhattan and Brooklyn, as well as parts of Bergen, Essex, Hudson, and Passaic Counties, officials said.