The incident occurred on the seafront at around 16:00 GMT on Sunday. While the woman managed to get out of the water safely, the man remains in the sea.
Coastguard rescue teams from Burnham and Weston-Super-Mare, as well as a coastguard helicopter, are participating in the search, using heat-seeking equipment to scour the water.
Lifeboats from RNLI Weston-Super-Mare are also involved in the search along the rivers Parrett and Brue. Avon and Somerset Police and the ambulance service are on the scene as well.