The Neshaminy Creek and Little Neshaminy Creek in Bucks County went over their banks, while the Wissahickon Creek in Fort Washington and Philadelphia and Crum Creek in Newtown Square also rose above flood stage, the National Weather Service said.
Minor flooding was expected overnight along the east branch of the Brandywine Creek below Downingtown.
The weather service issued a flood warning and flash flood watch for areas southwest of Harrisburg to northeastern Pennsylvania, and said the region could get another inch or two of rain by Saturday morning.
Rain fell heavily at times throughout the day Friday and washed out Sprint Cup qualifying at Pocono Raceway, as cars never got on the track.
Philadelphia International Airport said departing flights and arrivals were delayed because of the weather.