The geography of Puerto Rico encompasses the geographical features of Puerto Rico, a Caribbean archipelagic and island nation centered around a collective identity based on its land, history, ethnicity, culture, and language, and organized as a self-governing unincorporated territory of the United States. Located between the Greater and Lesser Antilles in the northeastern Caribbean Sea, east of Hispaniola, west of Saint Thomas, north of Venezuela, and south of the Puerto Rico Trench, it consists of the eponymous main island of Puerto Rico and 142 smaller islands, islets, and cays, including San Juan Islet in the north, Vieques and Culebra islands in the Virgin Islands, and Palominos island and Icacos cay in La Cordillera nature reserve in the east, Caja de Muertos island in Caja de Muertos reserve, and Caracoles and Media Luna cays in La Parguera reserve in the south, and Mona, Monito, and Desecheo islands in the Mona Passage in the west.

Measuring 177 km (110 mi; 96 nmi) in length and 65 km (40 mi; 35 nmi) in width with a land area of 8,868 sq km (3,424 sq mi), the main island of Puerto Rico is the 4th largest in the Caribbean, 29th in the Americas, and 81st in the world, making it the 170th largest country or dependency by surface area. With 3.2 million residents, it is also the 4th largest in the Caribbean, 4th in the Americas, and 31st in the world, making it the 136th largest country or dependency by population.

Geologically separated from the Greater Antilles island of Hispaniola by the Mona Passage and from the Lesser Antilles island arc by the Anegada Passage, the main island of Puerto Rico, the Spanish Virgin Islands of Vieques and Culebra, the British Virgin Islands, and the U.S. Virgin Islands except for the southernmost island of Saint Croix all lie on the same carbonate platform and insular shelf, the Puerto Rico Bank, between the Puerto Rico Trench in the North Atlantic Ocean and the Muertos Trough in the northeastern Caribbean Sea. The archipelagos of Puerto Rico and the Virgin Islands except for Saint Croix also lie on the same tectonic plate, the Puerto Rico–Virgin Islands microplate.

Around 60% mountainous, the main island of Puerto Rico has one principal mountain range covering the central region of the island from west to east, the Cordillera Central. It is divided into three subranges: the eponymous main subrange of Cordillera Central in the center, the Sierra de Cayey in the southeast, and the Sierra de Luquillo in the northeast. The highest elevation point in Puerto Rico, Cerro de Punta (4,390 feet or 1,338 meters), is located in the Cordillera Central, while El Yunque, one of the most popular peaks in Puerto Rico, located in the Sierra de Luquillo and part of El Yunque National Forest, has a maximum elevation of 3,540 feet (1,080 m).

The main island has seven valleys: Caguas, Yabucoa, Lajas, Añasco, the Coloso and Culebrinas, Cibuco, and Guanajibo. It has two narrow coastal plains: one stretching alongside the northern coast, and the other alongside the southern coast. The capital, San Juan, and its metropolitan area are located on the northern coastal plain in the northeast. It also has one prominent karst formation in its northwestern central region called the Northern Karst Belt, and two prominent batholiths, one in the southeastern municipality of San Lorenzo, and the other in the western municipality of Utuado. The island has 47 major rivers, of which the longest is Río de la Plata, and 26 reservoirs, lagoons, or lakes, among which is Laguna Grande (''big lagoon''), one of three bioluminescent bays in the archipelago of Puerto Rico located in the far northeastern municipality of Fajardo.

The archipelago of Puerto Rico has numerous protected nature areas, including the nature reserves of La Cordillera in the Sonda de Vieques (Vieques Sound) and Media Luna (''half moon'') in Lajas, the wildlife refuge in Cabo Rojo and Desecheo, the estuarine research reserve of Bahía de Jobos in Salinas, and the national park of the El Yunque forest in Rio Grande.

Puerto Rico is mostly mountainous with large coastal areas in the north and south. The main mountain range is called Cordillera Central (Central Mountain Range). The highest elevation in Puerto Rico, Cerro de Punta at 4,393 feet (1,339 m), is located in this range. Another important peak is El Yunque, the second highest peak in the Sierra de Luquillo at the El Yunque National Forest, with an elevation of 3,494 ft (1,065 m).

Puerto Rico is composed of Cretaceous to Eocene volcanic and plutonic rocks, which are overlain by younger Oligocene to recent carbonates and other sedimentary rocks. Most of the caverns and karst topography on the island occurs in the northern Oligocene to recent carbonates. The oldest rocks are approximately 190 million years old (Jurassic) and are located at Sierra Bermeja along the Lajas Valley in the southwest part of the island. These rocks may represent part of the oceanic crust and are believed to come from the Pacific Ocean realm. Puerto Rico lies at the boundary between the Caribbean and North American plates. This means that it is currently being deformed by the tectonic stresses caused by the interaction of these plates. These stresses may cause earthquakes and tsunamis. These seismic events, along with landslides, represent some of the most dangerous geologic hazards in the island and in the northeastern Caribbean. The most recent major earthquake occurred on October 11, 1918, with seismic moment estimated at 7.5 on the moment magnitude scale. It originated off the coast of Aguadilla and was accompanied by a tsunami.