Houston, the most populous city in the Southern United States, is located along the upper Texas Gulf Coast, approximately 50 miles (80 km) northwest of the Gulf of Mexico at Galveston. The city, which is the ninth-largest in the United States by area, covers 601.7 square miles (1,558 km²), of which 579.4 square miles (1,501 km²), or 96.3%, is land and 22.3 square miles (58 km²), or 3.7%, is water.

Houston is located in the Gulf Coastal Plain biome, and its vegetation is classified as temperate grassland. Much of the city was built on marshes, forested land, swamp, or prairie, all of which can still be seen in surrounding areas.

The city's topography is very flat, making flooding a recurring problem for its residents. The city stands about 50 feet (15 m) above sea level—the highest area within city limits being 90 feet (27 m). However, subsidence, caused by extensive groundwater pumping and resource extraction, has caused the elevation to drop 10 feet (3.0 m) or more in certain areas. As a result, the city turned to surface water sources for its municipal supply, creating reservoirs such as Lake Houston and Lake Conroe (of which Houston owns two-thirds interest).

Houston has four major bayous passing through the city: Buffalo Bayou, which runs into downtown and the Houston Ship Channel; and three of its tributaries: Brays Bayou, which runs along the Texas Medical Center; White Oak Bayou, which runs through the Heights and near the northwest area; and Sims Bayou, which runs through the south of Houston and downtown Houston. The ship channel goes past Galveston and into the Gulf of Mexico.

Houston is located 165 miles (266 km) east of Austin, 112 miles (180 km) west of the Louisiana border, and 250 miles (400 km) south of Dallas. Houston County, Texas, located 100 miles (160 km) north of Houston, is unrelated to Houston.

Houston is largely located within the Northern Humid Gulf Coast Prairies level IV ecoregion (34a), a subset of the Western Gulf coastal grasslands level III region as defined by the United States Environmental Protection Agency. This region is generally underlaid by Quaternary-aged sand, silts, and clays (clay, clay loam, or sandy clay loam) and covered by grasslands with occasional clusters of oak trees.

The land surface in and around the city of Houston is composed of alternating layers of red, gray, sandy brown, and black organic clay; these strata generally dip to the southeast at a slope of 0.06% (3 feet (0.91 m) of vertical change for every 1 mile (1.6 km) of distance traveled). These soils were deposited by tributaries of local waterways, particularly the Brazos and Trinity rivers. There is a considerable contrast in soil composition to the north around Cypress Creek; most of the surface there consists of tan-colored sand with small amounts of gray clay. The north and northwestern regions of Houston and Harris County feature a slightly steeper slope than other parts of the city, with occasional escarpments caused by faulting or erosion.

The sedimentary layers underneath Houston ultimately extend down some 60,000 feet (18,000 m), with the oldest beds deposited during the Cretaceous. Between 30,000 feet (9,100 m) and 40,000 feet (12,000 m) below the surface is a layer of salt, the primary source of salt domes that dot the metropolitan area. Since salt is more buoyant than other sediments, it rises to the surface, creating domes and anticlines and causing subsidence due to its removal from its original strata. These structures manage to capture oil and gas as it percolates through the subsurface; Pierce Junction is a notable example of a heavily drilled salt dome oil field in Houston.