The actively deforming Clear Lake basin has been shaped primarily by shear and tensional stresses within the broad San Andreas fault system; and it has been modified both by eruption and subsidence of the Clear Lake Volcanics and by depositional processes. Within the San Andreas fault system, shear has been dominantly right-lateral N35°W to N45°W, and maximum tension dominantly east-west. However, the current local maximum tension deduced from focal-plane solutions is N70°W, representing a secular change of unknown, possibly short duration, that could modify tensional basin-forming processes. The Collayomi fault zone (N45°W) partially bounds the basin on the southwest. The seismically active Konocti Bay fault zone (N25°W) across the basin merges into the less well documented N40°W Clover Valley fault zone that includes the faults in Clover Valley and near Lucerne and shorter faults near Clearlake Highlands and Lower Lake. The northeast margin of the main lake and both margins of the Oaks arm are largely fault-controlled; the Highlands arm is partly fault-controlled.

East of the basin, sediments now assigned to the Cache Formation—ranging in age from more than 1.8 to about 1.6 m.y. old—were deposited in an earlier basin that was controlled mainly by N35-45°W (Bartlett Springs) and N20°E (Cross Spring) fault zones. The earliest stage of the present Clear Lake basin is dated by the 0.6-m.y.-old rhyolite of Thurston Creek, which is found at or near the base of lacustrine-fluvial deposits. The extensive rhyolite’s thickness and distribution suggest that its eruption triggered subsidence that initiated or accelerated basin formation. Limited data suggest that a dominantly volcanic subsidence feature within the larger Clear Lake Basin could have had dimensions of about 13 by 15 km and either an elliptical shape with major axis oriented west-northwest, or a rectilinear shape. Volcanism occurring between 0.6 and 0.3 m.y. ago partly filled the southern part of the Clear Lake basin with flows, pyroclastic materials, and clastic deposits. Deposition beneath Clear Lake (0.4 mm/yr for the past 0.45 m.y.) has kept pace with subsidence and tilting down to the northeast. Projected maximum sedimentary and volcanic thicknesses could total more than 1 km beneath Clear Lake, suggesting a possible overall subsidence rate of 1.7 mm/yr for the past 0.6 m.y.