Punishing storms made their way through the region Thursday, contributing to the deaths of three people — including two young children — in Southeastern Pennsylvania and spawning a tornado in South Jersey.

A pregnant woman and her 9-year-old son were killed when their car was swept away in Berks County flash flooding as the drenching storms moved through. The storms were also blamed in part for the drowning of a 5-year-old at a Berks County farm.

The storms also triggered flooding and numerous water rescues across the area and spawned a tornado in South Jersey, less than a mile from where another twister touched down last weekend.

The Berks woman, who was eight months pregnant, called 911 about 4:30 p.m. to report that she and her son were trapped in their Mazda 3 with water rushing in, Douglass Township Police Chief John Dzurek told the Reading Eagle.

The woman’s cell phone indicated the car was located on Pine Forge Road near where Ironstone Creek flows into the Manatawny Creek, an area about 35 miles northwest of Philadelphia where at least five inches of rain had already fallen, Dzurek said.

The car with the mother and son inside was found about a half-mile away on an embankment of the Manatawny Creek, a tributary that feeds the Schuylkill, around 9:45 p.m., officials said.

They were identified Friday as Pamela Vera Snyder, 31, and her son, Preston Dray.

Preston was a student at Pine Forge Elementary School, where counselors were being made available Friday and Monday, Boyertown Area School District superintendent Dana Bedden wrote in a message to students and parents.

Snyder’s fiance, Joshua Knarr, told the Reading Eagle that a baby shower was planned for Sunday for Snyder, who was expecting a girl.

Friends and relatives expressed grief in postings on social media.

“We are numb at this point and can’t believe this is happening,” Knarr’s mother wrote on Facebook.

A 5-year-old boy also drowned around 8 p.m. Thursday in a rain-swollen retention pond on a farm in Oley, about 50 miles northwest of Philadelphia.

The boy, whose name was not released, was playing with other children when he got into a kayak that overturned in the pond, said Detective Sgt. Deron Manndel of the Central Berks Regional Police Department.

The boy’s father was trying to resuscitate the child when rescue personnel arrived and efforts continued while the boy was taken to Reading Hospital-Tower Health, but he was pronounced dead, Manndel said.

During the downpours in Berks and Montgomery Counties, the National Weather Service issued its first flash flood emergency since 2011 and its second-ever in the Philadelphia region, warning about the dangers posed by the rising water.

No further rain fell Friday but flood warnings remained in effect for much of the day along the Schuylkill, French Creek, and the Perkiomen Creek.

Philadelphia and its western and northern suburbs were hit by widespread flooding as heavy rains swept through Thursday afternoon and evening, leading to numerous calls for water rescues.

William Turner, deputy director for Emergency Management in Chester County, said fire-rescue teams were dispatched to 12 calls in the county.

Roadways along the Schuylkill remained flooded Friday morning, including Kelly Drive in Philadelphia.

No other serious injuries were reported, though the storms caused damage, including to a fleet of boats built by students and used by the public at Bartram’s Garden. More than a dozen boats were damaged or missing after becoming unmoored amid the unexpectedly high river flow on the Schuylkill. Free boating offered for Saturday was canceled.

Nearly eight inches of rain fell in Reading Thursday, while Philadelphia recorded 1.36 inches, according to the National Weather Service.

The weather service also said Friday that an EF-1 tornado with maximum wind speeds of 90 mph touched down in Mount Laurel, Burlington County, during Thursday’s storms.

The twister touched down less than a mile from where an EF-0 twister flipped a parked car last Saturday.

The latest tornado, which had a maximum path width of 150 yards, caused no injuries but traveled about 1.3 miles, uprooting trees and damaging some buildings in the township’s Ramblewood section, including its golf course.

One weather forecaster remarked on how rare it was to have two tornadoes less than a week apart in Mount Laurel, or along the entire Eastern Seaboard for that matter.

“Shoot, if the first one was longer, they could have crossed paths,” said Tony Gigi, a former weather service meteorologist who lives in Mount Laurel. (Fortunately for him, he lives on the other side of town.)

So far five tornadoes have been confirmed this year in New Jersey, according to David Robinson, the Rutgers University professor who is the state climatologist, “not that these have been large storms.” The annual average for the state is between two and three, he added.

Staff writers Frank Kummer and Anthony R. Wood contributed to this article.