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.

Starfish Garden is a sloping bank that transitions into a rocky reef, located 1200 metres offshore from Manuel Antonio. This site is suitable for beginners, with depths ranging from 6 to 18 metres and an average depth of 12 metres. Divers typically experience mild currents and visibility between 5 and 15 metres. Access is by boat only, with dives lasting approximately 45 minutes. The topography features a rocky reef structure, though divers should be aware of sharp coral present in the area. Water temperatures remain consistent throughout the year, ranging from 26 to 28 degrees Celsius.

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.

Las Gemelas consists of two prominent volcanic rock islets located offshore from Manuel Antonio. These formations function as a natural reef, providing a habitat for various marine life. The site is suitable for beginners and is accessed via boat. Depths range from 10 to 18 metres, with visibility varying between 8 and 30 metres. Conditions generally feature mild currents, though divers and snorkellers should be aware of potential surge, sharp coral, and sea urchins. Water temperatures remain warm throughout the year, typically between 28 and 30 degrees Celsius. Guided tours and equipment rentals are available for those visiting the area.

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.

El Toro is a pinnacle and reef site located 5000 metres off the coast of Manuel Antonio. The topography consists of rock and reef formations interspersed with sand patches. Divers can expect depths ranging from 5 to 35 metres, with an average depth of 18 metres. This site is suited for intermediate divers and requires boat access. Conditions vary significantly, with visibility between 6 and 30 metres and moderate currents. Divers should be prepared for surge and frequent, intense thermoclines that can cause temperatures to drop to 16 degrees Celsius, despite average water temperatures of 25 to 27 degrees Celsius.

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.