Milpitas is situated in the northeastern corner of the Santa Clara Valley, effectively acting as a bridge between the South Bay and the East Bay. The city's western edge approaches the southern marshlands of the San Francisco Bay, though it is largely separated from the water by the neighboring city of San Jose and various wetlands.
The city's geography is sharply divided between the flat, urbanized valley floor to the west and the rugged, undeveloped Diablo Range foothills to the east. Several key waterways flow through the city, including Coyote Creek, which forms part of the western border, and Penitencia Creek. The physical geography of Milpitas makes it a natural chokepoint for regional transportation, heavily influencing its development as a transit and industrial hub.