The Bay Islands , arrayed in an arc between 29 and 56 kilometers off the Caribbean coast of Honduras , are the above-water expression of the Bonacca Ridge, an extension of the mainland Sierra de Omoa mountain range that disappears into the ocean near Puerto Cortés .
The Bonacca Ridge forms the edge of the Honduran continental shelf in the Caribbean. Thus, on the northern, ocean-facing side of the three main islands, shallow waters extend only just beyond the shore before disappearing over sheer underwater cliffs to the deep waters, while on the south side the waters fronting the Honduran mainland are much shallower.
The height of the islands generally increases west to east, from the lowland swamps of Utila  to the modest mid-island ridges of Roatán  to two noteworthy peaks on Guanaja , the highest being 412 meters.
Ecological zones in the Bay Islands include pine and oak savannah, arid tropical forest, beach vegetation, mangrove swamp, and iron shore, or fossilized, uplifted coral. Much of the once-dense native pine and oak forests has not survived centuries of sailors seeking masts, immigrants looking for building material, and hunters setting fires to scare game.
The only forests left are on the privately owned island of Barbareta and in a few remote sections of Roatán, like by Brick Bay or around Port Royal . What was left of the famed forests of Guanaja was utterly flattened by Hurricane Mitch’s 290-kph winds—the island’s vegetation has only recently begun to recover.
Many of the once-abundant animal species endemic to the Bay Islands  have been hunted to extinction or to the brink of it: Manatees, seals, fresh- and saltwater turtles, white-tailed deer, green iguanas, basilisk lizards, boa constrictors, yellow-crowned and red-lored Amazon parrots, frigate birds, brown pelicans, and roseate terns have all vanished or are now seen only rarely. Crocodiles were once frequently seen crossing streets in Utila, but when one was spotted (and promptly killed) in December 1995, the event was a major local news item.
In spite of the depredations of hunters, 15 species of lizard still survive on the islands, along with 13 species of snake (including the poisonous but rarely seen coral), wild pigs, the small rat-like agouti, two species of opossum, and 13 species of bat. More than 120 bird species, most of which are migratory, have been spotted on the islands. Once at least 27 species of macaws, parrots, and parakeets lived on the islands; now the only macaws found are pets, and only about half the parrot species still survive in the wild.
The Bay Islands Conservation Association (BICA, www.bicautila.org ), with offices on all three islands, coordinates efforts to protect different endangered species as well as the islands’ remaining forests by overseeing reserves at Port Royal  and Carambola in Roatán , Turtle Harbour in Utila , and, supposedly, the entire island of Guanaja . BICA now also oversees the entire reef around Utila with a marine patrol, except for the shallow waters around the cays, from which only the fishermen of the cays can fish. They’ve also been active in Utila distributing environmentally friendly bug spray, doing bird surveys, and conducting ecotours.
The Bay Islands  have a superbly comfortable climate, with year-round air temperatures ranging 25–29°C (77–84°F) and east–southeast trade winds blowing steadily most of the year. Temperatures average 27°C (81°F) in the daytime, 21°C (70°F) at night—hot but not stifling during the day, and pleasant for sleeping at night.
Annual rainfall averages 220 centimeters, more than half of this coming in October and November, the height of the hurricane season. Water visibility is best when there is the least rain, usually March–September. Water temperature ranges from 26°C (79°F) midwinter to 30°C (86°F) in summer. The rains usually start in summer, often in June, and continue until December or January. February and March are usually the driest months. However, weather patterns vary widely from year to year, and rain can hit at any time.