San Jose has 127 elementary, 47 middle, and 44 high public schools. Public education in the city is provided by four high school districts, fourteen elementary districts, and four unified school districts (which provide both elementary and high schools).

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Private schools in San Jose are primarily run by religious groups. The Catholic Diocese of San Jose has the second largest student population in the Santa Clara County, behind only SJUSD; the diocese and its parishes operate several schools in the city, including five high schools: Archbishop Mitty, Bellarmine College Prep, Notre Dame, Saint Francis, and Presentation.

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San José State University is the oldest public university on the West Coast and the founding campus of the California State University system.

Other private high schools include two Baptist high schools, one non-denom Protestant school, one university-prep, a nonsectarian K-12 Harker School, and an Evangelical Lutheran school.

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.

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San Jose possesses about 15,950 acres (6,455 ha) of parkland in its city limits, including a part of the expansive Don Edwards San Francisco Bay National Wildlife Refuge. The city's oldest park is Alum Rock Park, established in 1872. In its 2013 ParkScore ranking, The Trust for Public Land, a national land conservation organization, reported that San Jose was tied with Albuquerque and Omaha for having the 11th best park system among the 50 most populous U.S. cities.

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A 2011 study by Walk Score ranked San Jose the nineteenth most walkable of fifty largest cities in the United States. 

San Jose's trail network of 60 miles (100 km) of recreational and active transportation trails criss-cross the city.

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In 2011 a small number of Chinook salmon returned to the Guadalupe River after 20 years and were filmed spawning under the Julian Street bridge. 

Conservationist Roger Castillo, who discovered the remains of a mammoth on the banks of the Guadalupe River in 2005, found that a herd of tule elk had returned to San Jose and recolonized the hills to the south, east of Highway 101, in early 2019.