Most Philadelphia roads and streets are expected to be open for Friday morning's rush hour, but several will remain closed, including Kelly Drive and Bells Mill Road.
SEPTA spokesman Andrew Busch said crews were repairing washouts that had undermined tracks in several areas and were clearing mud slides in the Jenkintown area that had washed mud, debris, and branches over tracks on several lines.
Auto traffic for Thursday's evening rush appeared relatively light, though there were pockets of congestion.
State Department of Transportation crews were clearing a mud slide from lanes of the Schuylkill Expressway near Girard Avenue on Thursday evening.
Thousands of commuters were stuck in traffic or stranded at train stations, unable to get to work or to return home.
Jenny Robinson, a spokeswoman for AAA Mid-Atlantic, said she struggled to get to Center City from her home in Doylestown after SEPTA canceled train service.
She took to her car, but traffic on Route 309 was slowed to a crawl by flooded turnpike access ramps at Fort Washington. She eventually completed her trip from SEPTA's Wyndmoor station on the Chestnut Hill East line.
Debris floated in the Delaware River as cars inched through standing water on Columbus Boulevard just south of the Ben Franklin Bridge.
Tow-truck drivers responding to calls for help found themselves stranded, often with a car on the hook.
"Our volume has been comparable to a cold winter day, but on a cold winter day, you can move around," said Perry Stanger, manager of roadside assistance for AAA Mid-Atlantic.
By 4 p.m., AAA had towed 483 cars and responded to 1,021 calls for assistance.
One tow-truck driver sat without moving in Broad Street traffic for two hours in North Philadelphia, said lead dispatcher Dan DiMuzio.
At least 28 state roads in the five-county Southeastern Pennsylvania region were closed by flooding and storm damage, PennDot said.
South Jersey commuters had troubles, too, facing major backups on Route 73 from Mount Laurel to the Betsy Ross Bridge.
More than 175 New Jersey road closures or restrictions were caused by the latest storm, including half a dozen in Gloucester and Camden Counties.
"It's been a slog," said Joseph Dee, spokesman for the New Jersey Department of Transportation. "Our crews got on top of the incidents from Irene, caught their breath, and went right back at it with this one."
Two Delaware River bridges north of Philadelphia were closed: The bridge linking New Hope and Lambertville, N.J., was damaged by floating trees and debris, and the bridge between Solebury, Pa., and Stockton, N.J., was shut when adjacent roads were inundated.
Several small bridges in Bucks County were also closed for much of the day Thursday.
West and north of Philadelphia, matters were even worse.
The Pennsylvania Turnpike was closed Thursday afternoon for 40 miles between the Reading and Harrisburg exits because of flooding. I-80 was closed between Exits 232 and 236, and I-81 was closed between Exits 90 and 100, PennDot said.
"Also, hundreds of secondary roads are closed," PennDot said. "Many roads that are open are experiencing extremely high traffic, resulting in gridlock in many regions. In addition to flooding, mud slides and downed trees continue to pose safety risks along roadways in the rain-drenched regions."
Amtrak service between Philadelphia and Harrisburg, which had been just been restored after the Irene flooding, was limited again Thursday by high water.
Contact staff writer Paul Nussbaum at 215-854-4587 or email@example.com.
Inquirer staff writer Robert Moran contributed to this article.