Topography of San Jose, California

The Guadalupe River runs from the Santa Cruz Mountains (which separate the South Bay from the Pacific Coast) flowing north through San Jose, ending in the San Francisco Bay at Alviso. Along the southern part of the river is the neighborhood of Almaden Valley, originally named for the mercury mines which produced mercury needed for gold extraction from quartz during the California Gold Rush as well as mercury fulminate blasting caps and detonators for the U.S. military from 1870 to 1945. East of the Guadalupe River, Coyote Creek also flows to south San Francisco Bay and originates on Mount Sizer near Henry W. Coe State Park and the surrounding hills in the Diablo Range, northeast of Morgan Hill, California.

Most of the city is made up of southern coastal scrub community, with dominant species being Artemisia californica, Eriogonum fasciculatum, Mimulus aurantiacus, various Salvia species, and Sambucus nigra. Southern oak woodland is the second most common vegetation community within the area, with prominent species being Quercus agrifolia. Other tree species found in the area include Plantanus racemosa, several willows, Juglans californica, Fraxinus spp., Juglans californica, Elymus triticoides and Quercus agrifolia.

The lowest point in San Jose is 13 ft (4.0 m) below sea level at the San Francisco Bay in Alviso; the highest is 2,125 ft (648 m). Because of the proximity to Lick Observatory atop Mount Hamilton, San Jose has taken several steps to reduce light pollution, including replacing all street lamps and outdoor lighting in private developments with low pressure sodium lamps. To recognize the city's efforts, the asteroid 6216 San Jose was named after the city.

There are four distinct valleys in the city of San Jose: Almaden Valley, situated on the southwest fringe of the city; Evergreen Valley to the southeast, which is hilly all throughout its interior; Santa Clara Valley, which includes the flat, main urban expanse of the South Bay; and the rural Coyote Valley, to the city's extreme southern fringe.

The extensive droughts in California, coupled with the drainage of the reservoir at Anderson Lake for seismic repairs, have strained the city's water security. San Jose has suffered from lack of precipitation and water scarcity to the extent that some residents may run out of household water by the summer of 2022.