Subsequent eruptions from the Long Valley magma chamber were confined within the caldera with extrusions of relatively hot (crystal-free) rhyolite 700,000 to 600,000 years ago as the caldera floor was upwarped to form the resurgent dome followed by extrusions of cooler, crystal-rich moat rhyolite at 200,000-year intervals (500,000, 300,000, and 100,000 years ago) in clockwise succession around the resurgent dome. (USGS)

Calderas tend to form after a series of large eruptions. Usually a new volcano starts to grow inside, eventually covering it. (About.com: Geology)

Over the course of several hundred years following the creation of the caldera, rain and snow filled the basin to a depth of 1,943 feet (592 meters). Crater Lake today is the nation’s deepest lake. (Crater lake)