The natural ecosystems of the California Floristic Province face serious threats from human activities and development. Though a state, California's economy ranks among those of the top seven countries in the world, and it is the most populated and fastest growing state in the United States.

California supplies one-half of all the agricultural products consumed in the United States of America each year. Direct pressures on ecosystems include urbanization, pollution, habitat encroachment, expansion of large-scale agriculture, strip mining and oil extraction, invasive alien species, road construction, livestock grazing, logging, increasing use of off-road vehicles, and suppression of natural fires.

Human population pressures have rendered California one of the four most ecologically degraded states in the United States of America. Native grasslands and vernal pool habitats in the hotspot have been reduced to about one percent of their original extent by the conversion of natural lands to agricultural fields and livestock pasture, urban development, and the invasion of exotic grasses. The magnificent redwood forests, which once occupied 8,000 kilometers along the California coast, have been reduced by intensive logging operations to 15 percent of their original standing area during the last 150 years (although many of these stands have regenerated).

Other seriously threatened ecosystems include wetlands, riparian woodlands and southern maritime sage scrub, which have all been reduced to 10 percent or less of their original area. Wetlands are destroyed by land filling and the diversion of water for agricultural, industrial, and residential development. The reduction in wetlands has been accompanied by a subsequent decline in shellfish, fish, and waterfowl populations that depend on these habitats. Riparian forests face threats from logging, grazing, and development (having been reduced by about 90 percent), while coastal sage scrublands are threatened by housing development, commercial development, and the increasing use of off-road vehicles.

Today, about 25 percent of the original vegetation of the hotspot remains in more or less pristine condition.