The park contains a significant amount of forest and watershed related resources. In additional to coast redwoods and Douglas-fir, there is a fairly large grove of endangered Santa Cruz cypress (cupressus abramsinana) along Butano Ridge. Other major tree species include california wax myrtle, tan oak (once commercially harvested for tan bark), madrone, california bay laurel, big leaf maple, cayon live oak, coast live oak, and knobcone pine.

Pescadero Creek and Alpine Creek both contain steelhead trout (salmo gairdneri). Pescadero Creek also has a small and variable run of silver salmon (Oncorhynchus Kitsutch). The steelhead (a sea run rainbow trout) is far the most significant of these species. Both are listed as endangered by the state and federal agencies.

The park also provides nesting for the endangered Mabled murrelet.

Other significant species of wildlife include: black-tailed deer, raccoon, western gray squirrel, coyote, mountain lion, feral pigs are becoming a significant pest, causing erosion damage.

Pescadero Creek Park sits atop a deposit of natural gas and oil. Natural gas occasionally bubbles up through seams near Hoffman Creek producing a strong gas odor. Crude oil pools up in the channel of Tarwater Creek, and seeps into Jones Gulch Creek staining the rocks. Oil exploration was attempted in the 1970's but failed to hit the pool. Natural gas under San Mateo County has been estimated at 10 billion cubic feet but no exploration wells have been attempted in the park.

Prepare for a safe and enjoyable visit to Pescadero Creek Park and other San Mateo County Parks by being aware of your natural environment.