The agency says full service will resume at 3:30 p.m. Wednesday.
It had been suspended between Little Falls and Mountain Lakes.
There are ongoing signal problems because of earlier flooding in Trenton that halted service at New Brunswick.
NJ Transit says Northeast Corridor trains were subject to 10- to 15-minute delays at mid-afternoon Wednesday.
North Jersey Coast Line trains also can be up to 15 minutes late.
There's no rail service at Bound Brook because of flooding on the Raritan Valley Line.
Rail service on the Port Jervis Line is suspended due to flood damage between Suffern and Harriman. Buses are being used there.
Important Travel Information:
Before starting your trip, visit http://www.njtransit.com for up-to-the-minute service information. This information is also available by calling (973) 275-5555 or from broadcast traffic reports.
Allow plenty of extra time travel time. Delays and service changes are possible.
Listen closely to public address announcements at stations for late-breaking service information.