The Geysers-Clear Lake geothermal area encompasses a large dry-steam production area in The Geysers field and a documented high-temperature, high-pressure, water-dominated system in the area largely south of Clear Lake, which has not been developed. Both systems have been extensively studied with geophysical techniques, drilling, and geological mapping during the past 20 years. An updated view is presented of the geological/geophysical complexities of the crust in The Geysers-Clear Lake region in order to address key unanswered questions about the heat source and tectonics. Early geophysical interpretations used a gravity low centered in the area between Clear Lake and The Geysers to suggest that a large magma chamber existed at depths starting at about 7 km. This first-order assumption of a large magma chamber expressed in the gravity data was used as a guide in subsequent geophysical and geological interpretations. Drill-hole temperature evidence is strongly suggestive of a shallow, hot-intrusive body, but in this paper the complexities are documented of the geological and geophysical data sets that make it difficult to pinpoint the location of “magma” or hot, solidified intrusive material. Forward modeling, multidimensional inversions, and ideal body analysis of the gravity data, new electromagnetic sounding models, and arguments made from other geophysical data sets suggest that many of the geophysical anomalies have significant contributions from rock property and physical state variations in the upper 7 km and not from ”magma“ at greater depths. Regional tectonic and magmatic processes are analyzed to develop an updated scenario for pluton emplacement that differs substantially from earlier interpretations. In addition, a rationale is outlined for future exploration for geothermal resources in The Geysers-Clear Lake area.