According to the United States Census Bureau, the city has a total area of 601.7 square miles (1,558.4 km²); this comprises 579.4 square miles (1,500.7 km²) of land and 22.3 square miles (57.7 km²) of water.

Most of Houston is located on the gulf coastal plain, and its vegetation is classified as temperate grassland and forest. Much of the city was built on forested land, marshes, swamp, or prairie, which are all still visible in surrounding areas. Flatness of the local terrain, when combined with urban sprawl, has made flooding a recurring problem for the city. Downtown stands about 50 feet (15 m) above sea level, and the highest point in far northwest Houston is about 125 feet (38 m) in elevation. The city once relied on groundwater for its needs, but land subsidence forced the city to turn to ground-level water sources such as Lake Houston and Lake Conroe.

Houston has four major bayous passing through the city. Buffalo Bayou runs through downtown and the Houston Ship Channel, and has three tributaries: White Oak Bayou, which runs through the Heights neighborhood and towards downtown; Braes Bayou, which runs along the Texas Medical Center; and Sims Bayou, which runs through the south of Houston and downtown Houston The ship channel continues past Galveston and then into the Gulf of Mexico.