Three people drowned in the Gujjar Nullah on Friday and on Saturday morning, one body was found.
Rescue teams say they were swept into the drain by strong water currents as the area flooded due to heavy rain on Friday.
The civil administration has not started a search operation yet. The victims’ family have been searching the water themselves.
The victim whose body has been found has been identified as Nasir. His son Bilal and brother Adnan are still missing.
In a separate incident, a young man who fell in the same drain was rescued safe and sound by a group of onlookers.
Heavy rain hit Karachi on Friday, leaving several areas submerged.