Mono Lake occupies part of the Mono Basin, an endorheic basin that has no outlet to the ocean. Dissolved salts in the runoff thus remain in the lake and raise the water's pH levels and salt concentration. The tributaries of Mono Lake include Lee Vining Creek, Rush Creek and Mill Creek which flows through Lundy Canyon.

The basin was formed by geological forces over the last five million years: basin and range crustal stretching and associated volcanism and faulting at the base of the Sierra Nevada. Five million years ago, the Sierra Nevada was an eroded set of rolling hills and Mono Basin and Owens Valley did not yet exist.