Santa Cruz Island is the most topographically diverse of the Southern California Islands. It is rough and mountainous with deep canyons, and large areas of flat land are limited. Much of the northern shore is bold and rugged, with cliffs dropping to the sea and intersperses with small pocket beaches at the mouths of canyons. Longer stretches of beach are found along the western and southern shores. A large central valley is nestled between two mountain ranges for much of the island's length. Access into this valley is through a narrow, winding, stream filled canyon, three miles long. Picacho Diablo, at 2434 feet in elevation, is the highest point. Several other peaks surpass the 2000 foot mark on the island's north side.

The entire island has a Mediterranean climate. Cool, rainy winters and warm, dry summers. Due to the island's large size and varied topography, a number of microclimates exist. The coastal areas are mild throughout the year. Temperatures rarely rise above 85 degrees or below 35 degrees. However, the central valley may reach over 100 degrees or drop to 20 degrees in the winter.

The geology of Santa Cruz Island varies greatly. The oldest rocks are schists and other metamorphosed sedimentary rocks of pre-Cretaceous period, intruded by Cretaceous and Jurassic quartz diorites. These are found on the island's south side. The northern side of the island contains primarily Miocene volcanic rocks. Limited Pleistocene deposits are particularly well developed at Potato Harbor and on the island's east end.