Clear Lake is a natural freshwater lake in Lake County in the U.S. state of California, north of Napa County and San Francisco. It is the largest natural freshwater lake wholly within the state, with 68 square miles of surface area. It has an age of nearly 500,000 years. It is the latest lake to occupy a site with a history of lakes stretching back at least 2,500,00…Clear Lake is a natural freshwater lake in Lake County in the U.S. state of California, north of Napa County and San Francisco. It is the largest natural freshwater lake wholly within the state, with 68 square miles of surface area. It has an age of nearly 500,000 years. It is the latest lake to occupy a site with a history of lakes stretching back at least 2,500,000 years.