San Mateo is a comparatively small county that includes the vast majority of the San Francisco Peninsula. For such a small county, it also has a surprising diversity of habitats. By resting on the peninsula, it includes stretches of rugged coastline and open, sandy beaches along with coastal oak and redwood forests and scrublands. The majority of the population lives on the heavily developed bay side of the county, but even there, there are tracks of preserved estuary. The two sides are divided by the ecologically diverse Santa Cruz Mountains and at its northern end lies San Bruno Mountain, the bulk of which is in San Mateo County.

Numerous parks and reserves are found here, including Ano Nuevo State Park, the Fitzgerald Marine Reserve, Portola Redwoods State Park, and the Pillar Point tidepools. Every winter impressive numbers of gulls can be found in San Mateo County and many rare species have been found among these flocks.