From: Quirolo, 1998
Bahia Honda is approximately 35 miles west of Havana and is the first bay that cruising boats traveling west from Havana are allowed to enter. Navigational charts and cruising guides describe shallows as reefs, which can be found just outside the entrance of the bay. Honda is a rather large industrial bay where freighters and other large vessels are torn apart and recycled. This is also a port for loading dangerous cargoes, especially acids.

In 1998, Reef Relief began its first studies in an area called Ensenada de Las Salinas from a point at Punta del Morillo south to the guardia frontera post. The expedition found that the water inside of the bay was much greener than the water immediately outside of the bay and that algal coverage increased upon entering the bay. On the outside of the bay, fairly healthy sea grass beds covered the Ensenada de las Salinas, yet there were no fish, conchs, or sea urchins. A healthy sea grass field was found at the beginning of the first snorkel. On the outside of the bay however, a lack of fish and conch was noticed. As the team moved in toward the bay, algal blooms became prevalent: Sargassum helix and Chaetomorpha linum among others. It was obvious that a nutrient overload is pulsing out of the bay as the water color changed dramatically from deep Gulf Stream blue from the entrance of the harbor to an opaque green on the inside, a distance of less than one mile.

A reef located west of the entrance of the bay, a very shallow area, is subject to the majority of water flowing out of the bay due to the westerly set of the onshore current flowing westerly past the mouth of the bay. There were no sea urchins or fish of any size found and macroalgae dominated this reef. Several fresh boat grounding scars were evident one of which smashed into the only healthy brain coral, Diploria clivosa, in the area. A fresh water cenote with much cooler water than on the reef was discovered. The few formations of Elkhorn coral, Acropora palmata, in the bay were dead. It was of little surprise to find algae dominating this reef considering Bahia Honda is a port where dangerous chemicals are transferred.

At another point located just east of the entrance of the harbor, the area was very shallow and flat surrounded by sand and sea grass. There were very few large corals in the area, giving the impression that this area has always taken the brunt of heavy seas protecting the entrance to the bay. There was a wide diversity of small coral colonies, all of which were threatened by abundant macroalgae. In both areas, no healthy sea fans were found, and two men in snorkel gear were found spear fishing. This reef had a yellow turf dominating the bottom, similar to algae seen on the shallow reefs near Negril, Jamaica in Long Bay.