The main ridge of the San Joaquin Hills runs southeast from the Upper Newport Bay area, attaining its maximum height of roughly 1,000 feet (300 m) near Laguna Beach.

In many places, the San Joaquin Hills drop directly into the Pacific Ocean, creating the steep sea cliffs that characterize the region.

In the north, Newport Bay was formed by the Santa Ana River switching its course to the south, cutting across the northern part of the range.

[4] The native vegetation of the hills is in the California coastal sage and chaparral and California chaparral and woodlands ecoregions, largely coastal sage scrub, but other habitat types include grasslands, oak woodlands, wetlands, and riparian habitats along several streams.

[6] Prior to the arrival of Europeans in the area, residents of the nearby Tongva and Acjachemen village of Genga frequented the hills.