The waters around Contadora offer some of the best snorkelling and diving accessible from Panama City. Rock and coral formations ring most of the island's headlands, and visibility is typically 10–20 metres in the dry season. Common sightings include parrotfish, angelfish, butterfly fish, clownfish, red snapper, stingrays, and nurse sharks. Manta rays and whale sharks pass through the deeper water around the archipelago seasonally.
A PADI-certified dive centre operates on the island and offers introductory dives, certification courses, and guided dives to sites about 15 minutes offshore by boat. The dive sites around the nearby uninhabited islands in the Pearl Islands chain go deeper and see less traffic than the sites immediately around Contadora. Snorkelling gear is available for rent at the dive centre and from a couple of beach-side operators.