El Aquario is a reef site located 10 kilometres offshore from Manuel Antonio. The topography consists of a central sand patch surrounded by rock and reef pinnacles featuring hard coral formations. Divers can expect depths ranging from 8 to 25 metres, with an average depth of 18 metres. Conditions include mild currents and visibility between 5 and 15 metres. Water temperatures remain consistent, typically between 25 and 28 degrees Celsius. Access is by boat only, and the site is suitable for beginners. Hazards include jellyfish, lionfish, sharp coral, and stonefish. Species recorded around this area include wrasses, butterflyfish, rock cod, triggerfish, pufferfish, and spiny lobsters.

Pelican Island, or Isla Mogote, is a reef site located 5000 metres off the coast of Manuel Antonio National Park. This boat-accessible location offers depths ranging from 10 to 18 metres, with an average depth of 14 metres. Divers and snorkellers can expect variable visibility between 5 and 25 metres and moderate currents. Water temperatures remain consistent throughout the year, typically between 26 and 28 degrees Celsius. The site is suitable for beginners, though visitors should be aware of hazards including sea urchins and sharp coral. As a marine environment, the area supports a variety of reef habitats.

Geos Ridge is a series of rock ridges extending into the ocean off Manuel Antonio. The site features rocky outcrops and soft coral formations, with depths ranging from 6 to 43 metres and an average depth of 14 metres. Due to the moderate current, this site is suitable for drift diving and is accessible only by boat, located 5 kilometres from shore. Visibility varies between 6 and 30 metres. The site is open to both divers and snorkellers, with night diving available. Divers should be aware of the deep sections, sharp coral, and potential for strong currents.

Punta Catedral is the underwater extension of the prominent landmark within Manuel Antonio National Park. This site features dramatic volcanic rock formations and vertical walls that descend to depths of 1 to 5 metres, with an average depth of 3 metres. Divers and snorkellers can access the site from both shore and boat. Conditions vary, with visibility typically ranging between 3 and 10 metres and mild currents present. Due to the presence of rip currents and jellyfish, this site is best suited for advanced divers. Facilities available at the location include parking, toilets, and guided tours.

Playa Manuel Antonio is a calm water bay located within Manuel Antonio National Park, offering a shallow environment suitable for snorkelers. The site features a reef with depths ranging from 2 to 4 metres, averaging 3 metres. Entry is directly from the shore. Conditions include mild currents and visibility typically between 3 and 10 metres, which may decrease following heavy rainfall. Facilities available at the site include parking, toilets, showers, and changing rooms. Divers and snorkelers should be aware of potential hazards including rip currents, sea urchins, and sharp coral. The site is well-suited for beginners looking for a shallow, accessible experience.

South Point in Manuel Antonio features a diverse underwater topography consisting of a drop-off wall, a canyon, and reef structures. The site reaches depths between 5 and 30 metres, with an average depth of 18 metres. Access is by boat, located 3000 metres from the shore. Divers should be prepared for moderate currents and surge, with visibility ranging from 5 to 25 metres. Water temperatures typically sit between 25 and 27C, though cold thermoclines reaching 16C are frequently encountered. This site is suitable for beginners and offers a typical dive duration of 45 minutes.

The Turtle Trap, or La Trampa, is an archaeological site featuring a pre-Columbian stone semicircle designed to trap turtles. Located in Manuel Antonio, this site offers a shallow snorkel experience ranging from 1 to 8 metres, with an average depth of 4 metres. At low tide, the stone structure forms a distinct micro-habitat for various marine life. Snorkellers may encounter common species such as Sally Lightfoot crabs and other crabs, while less frequent sightings include snowflake morays, wrasses, spiny lobsters, triggerfish, threebanded butterflyfish, rock cod, barberfish, sea hares, hermit crabs, sergeants, yellow snappers, and yellowfin surgeonfish. Access is via the shore, and conditions typically feature mild currents and visibility between 3 and 10 metres.

Canyon Reef in Manuel Antonio features distinct canyon formations running along the back of the island. This site is suitable for intermediate divers, offering depths ranging from 5 to 30 metres with an average of 18 metres. Divers can expect mild currents and visibility between 15 and 30 metres. Water temperatures typically range from 25 to 27 degrees Celsius, though cooler currents can occasionally drop temperatures to 19 degrees Celsius between December and March. Access to this site requires a boat, and divers should be aware of potential surge conditions. A typical dive at this location lasts approximately 50 minutes.