Areas hit by flooding in South Jersey were spared heavy downpours overnight, allowing rain swollen waterways to begin to subside.

Still, a flood warning remained in place for the north branch of the Rancocas Creek near Pemberton, an area prone to flooding.

“We had some rain overnight, but not too much,” said Michael Silva, meteorologist at the National Weather Service’s Mount Holly office. “It had a minimal impact on the flooding.”

Waterways that overflowed their banks are “in the process of subsiding,” said Silva.

Late Thursday, officials were concerned heavy rains would add to the flooding that closed highways, paralyzed the PATCO High Speed Line, and forced the evacuation of residents along the Rancocas and Big Timber creeks.

Drenching downpours overnight Wednesday into Thursday — more than four inches fell at Philadelphia International Airport — caused a panoply of problems that prompted New Jersey Gov. Phil Murphy to declare states of emergency in Burlington, Camden, and Gloucester Counties.

“It’s pretty clear that Mother Nature is shifting toward us, not away from us," Murphy said during an afternoon press conference at the Cherry Hill Fire Department. "It’s more frequent and more intense.”

Throughout the day, the governor traveled to the affected counties in South Jersey, thanking first responders who worked through the early morning hours. In Cherry Hill, local officials pledged to fight for federal dollars to repair damaged homes. Conversations with home owners in Burlington County, Murphy said, were tough. One young couple, he said, had tears welling in their eyes because of the damage to their homes.

Camden County Emergency Manager Coordinator Sam Spino said crews “are ready for whatever” and out in high-wheel vehicles to evacuate as needed.

During the governor’s press conference in Southampton, cell phone alarms signaling a flash flood warning broke up the meeting –– a sign of the weather to come.

“The concern, that we haven’t addressed until now,” Murphy said, “is that there’s more coming tonight.”

Scores of people were forced out of their homes Thursday morning and into rescue boats in Lumberton and Southampton townships due to the Rancocas overflowing. To the south in Westville, the rising Big Timber Creek led to the evacuation of 59 people who found their streets and homes surrounded by water.

In Southampton, where about 67 homes were affected by flooding, officials at the Vincent Fire Company were readying for another possible round of rescues if the new storms and a rising tide force residents who opted to stay in their homes previously to leave Thursday night.

“Everybody’s running home to take a nap and get ready for it,” one firefighter said.

In total, approximately 50 people and nearly 20 pets were evacuated in Southampton beginning Thursday early morning, according to township administrator Kathleen Hoffman.

In Gloucester County, emergency management manager Charles Murtaugh said officials also were keeping an eye on Greenwich Township, which is protected by a levee along the Delaware and experienced some flooding during the day.

Murtaugh also said the flooding in Westville, which sits where Big Timber Creek meets the Delaware, was the worst to hit the borough since 1988.

Not only did those places prone to flooding in South Jersey do so, such as along Cooper River in Camden County, but high waters closed a number of highways for hours, including I-295 in Bellmawr where it merges with Route 42 and I-76. At least one highway, Route 73, remained closed in Maple Shade into the afternoon.

Burlington County reported that flooding closed roads at more than four dozen locations. Camden County said fire departments responded to about 70 calls for occupied vehicles stuck in water by 7 a.m.

Before dawn, PATCO suspended all High Speed Line service between Lindenwold and Broadway in Camden after flooding washed away track ballast and water damaged some stations, forcing thousands of commuters to make other travel or work arrangements for the day.

Service resumed for all trains — including the water-damaged Ashland station — Thursday and returned to regular schedule in time for the evening commute.

The rains also downed trees and flooded roadways in Southeastern Pennsylvania, but that region appeared to have escaped the brunt of the overnight storms. Damage was reported in Montgomery County, where part of the roof collapsed at an Acme in Flourtown. No injuries were reported.

Flooding also closed several roads in Horsham Township, police said.

SEPTA reported no major problems during the morning rush hour.

The stalled system that has produced all the rain this week is expected to be pushed out of the way by an advancing cold front that will bring a sunny and comfortable weekend.

Staff writers Barbara Boyer, Anthony R. Wood, Jason Laughlin, and Oona Goodin-Smith contributed to this story.