Someone on the small vessel called 911 just after midnight on Thursday morning when they noticed water coming on board. There was another boat that stayed nearby while they were waiting for rescuers.
A police helicopter located the boats near the Platt Bridge in South Philadelphia.
The fire department marine unit and coast guard made sure everyone made it to shore safely.
Police say the 12 people are in their 20s and 30s, and are in good spirits.
It's unclear what caused the boats to spring a leak.
A previous version said people were rescued from two boats but it was determined that just one was taking on water.