Water damage caused by Thursday’s rain is wreaking havoc on the No. 7 subway this weekend.

The tunnel linking Queens and Manhattan was closed during last night’s rush hour, and service will be limited through the weekend while NYC Transit crews fix the problem.

Just one track will be open today and tomorrow between Queensboro Plaza and Times Square, on which NYC Transit will run a single back-and-forth shuttle train.

Thursday’s rain damaged the signal system in the tunnel, which takes the No. 7 beneath the East River, said MTA spokesman Kevin Ortiz.

Flooding also briefly shut a section of the Bronx River Parkway near Gun Hill Road yesterday.