Geologic forces have created the landscape of Pinnacles, but a climate of hot dry summers and winter rains has also shaped the terrain. The vegetation of the park transforms each year as the rain stops and temperatures climb; hillsides go from vibrant green to golden brown within days. Many of the chaparral plants thrive when fires burn through to make room for new growth. Streams that are dry throughout the summer can flood during the winter and spring rains.

Non-native species and development have also had an impact on the monument. Exotic species of both plants and animals have threatened the native vegetation and wildlife. Roads and trails have created erosion and affected sensitive riparian areas. Park managers are working to limit the damage caused by these factors.