Baja California has two sea shores. It borders the Pacific Ocean to the west and the Gulf of California to the east. Even though the state is not large in area, its geography is very diverse. The Sierra de Baja California (also known as the Peninsular Ranges) runs in the middle of the state with different denominations. The two most important are the Sierra de Juarez and the Sierra de San Pedro Martir. These ranges are home to forests similar to those in Southern California.

The Picacho del Diablo is the highest peak in the whole peninsula, offering spectacular views of the Gulf of California. Lying in between these mountain ranges, there are some valleys that are suitable for agriculture such as the Valle de Guadalupe and the Valle de Ojos Negros. The mild weather makes this area excellent for the production of citrus fruits and grapes. This area is also rich in minerals. The mountain range gets closer to the Gulf of California towards the south of the state and the western slope becomes wider, forming the Llanos del Berrendo in the border with Baja California Sur.

There are numerous islands on the Pacific shore. Guadalupe Island is the remote outpost to the west and it is home to big colonies of sea lions. In Cedros Island there is a small community living mostly on fishing. The Todos Santos Islands, in front of Ensenada, are popular with surfers offering some of the highest waves worldwide.

To the east, the Sonoran Desert enters the state from both California and Sonora. Some of the highest temperatures in Mexico are recorded in or nearby the Mexicali Valley in the northeast. However, with irrigation from the Colorado River, this area has become truly an agricultural center. The Cerro Prieto geothermical province is nearby Mexicali as well (this area is geologically part of a large pull apart basin); producing about 80% of the electricity consumed in the state and enough more to export to California. The Laguna Salada, a saline lake below the sea level lying in between the rugged Sierra de Juarez and the Sierra de los Cucapah, is also in the vicinity of Mexicali where there the state has been considering plans to revive the lagoon and are currently (2008) looking at a plan by SDSU Adj. Professor Newcomb (ICATS) to do this using his geothermal desalination system to supply water locally. SEMARNAT belives this to be the first viable plan presented. The highest mountain in the Sierra de los Cucapah is the Cerro del Centinela or Mount Signal. The Cucapah are the primary indigenous people of that area and up into the Yuma AZ area.

The state is also blessed with numerous beaches on its east coast. Fishing and touristic towns such as San Felipe and Bahia de Los Angeles are a major attraction for people in search of adventure, nice beaches and fresh fish. The area south of San Felipe is basically undeveloped and pristine beaches can be found in many bays. All of the islands in the Gulf of California, on the Baja California side, belong to the municipality of Mexicali.

The main source of water in the state are the Colorado River, which empties in the Gulf of California, (but now rarely reaches the Gulf) and the Tijuana River, serving the cities of Mexicali, Tecate, and Tijuana. The rest of the state depends mostly on wells and a few dams. Tijuana also purchases water from San Diego County's Otay Water District. Potable water is the largest natural resource issue of the state.