The drownings occurred in an area known as the Devil's Pool, KYW-TV reported. Swimming there is illegal, although the pool in the Roxborough neighborhood is popular with locals.
Chief Inspector Joseph Sullivan said the man was at the creek with his four children. The 13-year-old waded into the water and apparently got out of his depth.
"And we do what any good father would do, we see our young son in trouble and we don't think about ourselves. And we go in to the water, and unfortunately that resulted in a double tragedy," Sullivan said.
Both bodies were recovered by late afternoon.
Sullivan said the creek has sudden changes in depth and a strong current, making it dangerous for swimmers. Philadelphia bans swimming in all its waterways, although police say enforcement is difficult, given the miles of creeks and rivers in the city.
The Wissahickon rises in suburban Montgomery County and runs 23 miles to the Schuylkill River. The Wissahickon Gorge, part of Philadelphia's Fairmount Park system, is a famous natural landmark.