The benitoite deposit occurs in a large area of serpentine which extends many miles northward past the New Idria quicksilver mine and a few miles southward, and forms the summit of an anticlinal ridge pitching down to Coalinga. This serpentine is of the usual type of the Coast Ranges and presents different phases from hard dark-green and greenish-black material to softer lighter-colored rock containing more or less talcose and chloritic minerals. Slickenside seams and lentil-shaped blocks and masses are common through the serpentine, much of which is decomposed near the surface and breaks down to light grayish-green soil which has a greasy feeling when rubbed between the fingers. Inclusions of masses of schists and other rocks of the Franciscan formation occur in the serpentine. These schists may be micaceous or more basic, having common hornblende, actinolite, or glaucophane as characteristic minerals.

The benitoite deposit is located in one of these basic inclusions, a portion of which has a somewhat schistose structure, while the rest is nearly massive. These phases were probably originally different adjacent formations that have been metamorphosed. Part of the massive form is a dark-gray to greenish-gray rock that might be called trap. In some specimens the following minerals are determinable under the microscope: augite, plagioclase crushed and recrystallized and containing clinozoisite prisms, secondary albite, yellow serpentine, and a little titanite and pyrite. The rock is therefore a partly metamorphosed diabase or gabbro. The more schistose phases are grayish-blue to blue and grade into vein material. They are composed of one or more varieties of hornblende, some partially chloritized, with albite, and, near the vein, with natrolite. The hornblende occurs in minute needles, felted masses of needles, blades, and stouter prisms. These have a bluish to yellowish green to nearly colorless pleochroism, and are in part probably actinolite and in part glaucophane or allied hornblende. The natrolite fails and the albite is also less abundant in the hornblende rock at some distance from the vein.

The vein is a highly mineralized shattered zone in the schistose rock. The fractures and joints with the vein filling are about parallel with the schistosity of the rock, which averages nearly east and west in strike with local variations and has a varying dip of 20° to 70° N. A sketch map of a small area on the benitoite mine hill giving the outcrops with their dips and strikes and the formations encountered in the mine workings shows the schist and gabbro inclusion in the serpentine to be quite irregular in shape. The width at the mine between the serpentine walls is about 150 feet and at a distance of 150 feet east of the mine it is only about 90 feet; about 80 feet farther east at the apex it is over 100 feet. This schist inclusion has been described by Kalph Arnold as 150 feet wide at its widest point and at least 1,200 feet long.

The metamorphism of the schist inclusion has been of two kinds — first mashing and sheeting of the original basic rock producing schistosity and opening channels for solutions and then a passage of mineral-bearing solutions recrystallizing and replacing the minerals of the rock with albite. The albite permeated the rock for many feet each side of the fracture zone. The conditions of temperature or pressure of the solutions became changed, so that natrolite was next deposited. The natrolite did not permeate far into the rock, but formed a coating on the walls of the fissures. Neptunite and benitoite were formed with the natrolite at this stage in the fissures and openings but did not penetrate the wall rock. This whole mineralized zone containing many bands and masses of natrolite with gem minerals in the joints, fissures, and open spaces in the brecciated hornblende rock may be called the vein.

The unfilled cavities and seams in the vein zone aided by later fractures and faults has offered an easy passage for more recent decomposing meteoric waters. The latter have leached portions of hornblende schist along and included in the vein, have removed part of the minerals of the vein, and have stained the natrolite on the walls of the cavities and seams with iron and manganese oxides. The rock, leached of albite, has a more or less porous texture and is composed principally of fine fibrous blue hornblende and actinolite.