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.
The California myotis may be active at any time of year, although activity is greatly reduced in winter. Roosts in small groups, or singly. The California myotis mates in the fall. The young are born from late May-July, with a peak in early June. The single yearly litter averages one young.