Foraging flight is slow and highly maneuverable. Suitable crevices may be found in buildings, under bark, and in caves and mines. Open spots, especially in human-made structures, are used as night roosts. The California myotis roosts or hibernates in small groups, or singly. This species is less tied to the continual use of particular roosts than are other bats.
Individuals appear to use the nearest available night roost after feeding.
Small maternity colonies are found in crevices in buildings, mines, hollow trees, and other sites. This species has an ability to produce concentrated urine, but it drinks regularly. The California myotis prefers rock-walled canyons with open water, open woodlands and forests, or brushy habitats for foraging. There may be a second peak before sunrise. Activity also is reduced by heavy precipitation or strong winds.