
Bahía de Jobos or Reserva Natural de Investigación Estuarina de Bahía de Jobos is a federally protected estuary in Aguirre, Puerto Rico. The bay is an intertidal tropical ecosystem dominated by seagrass beds, coral reefs, and mangroves. In an area of 1140 hectares, the reserve contains five distinct habitat types and provides sanctuary to several endangered species. Bahía de Jobos is one of 28 reserves that comprise the National Oceanic and Atmospheric Administration’s (NOAA) National Estuarine Research Reserve System. The reserve is operated in conjunction with the Puerto Rico Department of Natural and Environmental Resources (DRNA).

Caja de Muertos is an uninhabited island off the southern coast of Puerto Rico, in the municipality of Ponce. The island is protected by the Reserva Natural Caja de Muertos natural reserve, because of its native turtle traffic. Hikers and beachgoers are often seen in the island, which can be reached by ferry from the La Guancha Boardwalk sector of Ponce Playa. Together with Cardona, Ratones, Morrillito, Isla del Frio, Gatas, and Isla de Jueyes, Caja de Muertos is one of seven islands ascribed to the municipality of Ponce.

El Toro Wilderness is a 10,000-acre (40.5 km2) National Wilderness Preservation System unit located partly within El Yunque National Forest on the island of Puerto Rico. El Toro, named after the highest peak in the forest at 3,524 feet (1,074 m), is the only tropical wilderness in the United States National Forest System. It was created in 2005 by the Caribbean National Forest Act of 2005.

El Yunque National Forest, formerly known as the Caribbean National Forest, is a forest located in northeastern Puerto Rico. It is the only tropical rainforest in the United States National Forest System and the United States Forest Service.

Isla de Jueyes are a group of three small uninhabited islands off the southern coast of Puerto Rico. Together with Caja de Muertos, Gatas, Morrillito, Ratones, Cardona, and Isla del Frío, Isla de Jueyes is one of seven islands ascribed to the municipality of Ponce. At an area of just 2.89 cuerdas, they are also the smallest of these seven islands. Like Isla del Frío, the islands are considered part of barrio Vayas.

Mona is the third-largest island of the Puerto Rican archipelago, after the main island of Puerto Rico and Vieques. It is the largest of three islands in the Mona Passage, a strait between the Dominican Republic and Puerto Rico, the others being Monito Island and Desecheo Island. It measures about 7 miles by 4 miles, and lies 41 mi (66 km) west of Puerto Rico, of which it is administratively a part. It is one of two islands that make up the Isla de Mona e Islote Monito.

Isla de Ratones also known as Cayo Ratones or Isla Ratones is a small island located near the Joyuda Lagoon in Cabo Rojo, Puerto Rico. The island is a popular spot for snorkeling and bathing.
The Luquillo Experimental Forest is a protected area of tropical rainforest in northeastern Puerto Rico. The experimental forest is located in the Sierra de Luquillo some 50 km (30 mi) east of San Juan, the capital of the island. It is a UNESCO Biosphere Reserve and is used for research into silviculture, forest regeneration, and other purposes.

Morrillito is a small uninhabited island off the southern coast of Puerto Rico. The island is protected by the Reserva Natural Caja de Muertos natural reserve because of its native turtle traffic. Together with Caja de Muertos, Gatas, Ratones, Cardona, Isla del Frio, and Isla de Jueyes, Morrillito is one of seven islands ascribed to the municipality of Ponce.