Around 195 subspecies have been described, mostly on the basis of geographical distribution. Some of these have previously been described as distinct species in their own right.
Botta's pocket gopher is strictly herbivorous, feeding on a variety of plant matter. Shoots and grasses are particularly important, supplemented by roots, tubers, and bulbs during the winter. An individual often pulls plants into the ground by the roots to consume them in the safety of its burrow, where it spends 90% of its life.
The metabolic rate, consumption rate and amount of energy assimilated for non-reproductive adult gophers is consistent through winter, spring, summer and fall. The average adult Botta's pocket gopher has a body temperature of 36 °C (97 °F). Burrowing can be extremely energetically demanding requiring between 360 and 3,400 times as much energy as moving across the surface, depending on soil density. Due to the high cost of burrowing, Botta's pocket gopher is good at conserving energy by having a low basal metabolic rate and thermal conductance.
The main predators of this species include American badgers, coyotes, long-tailed weasels, and snakes, but other predators include skunks, owls, bobcats, and hawks. This species is considered a pest in urban and agricultural areas due to its burrowing habit and its predilection for alfalfa; however, it is also considered beneficial as its burrows are a key source of aeration for soils in the region.
Digging by Botta's pocket gophers is estimated to aerate the soil to a depth of about 20 cm (7.9 in), and to be responsible for the creation of Mima mounds up to 2 m (6 ft 7 in) in height. Populations of the species have been estimated to mine as much as 28 tonnes of soil per hectare per year, much of which is moved below ground, rather than being pushed up into the mounds. The species also has been associated with the deaths of aspen in Arizona and creates patches of bare ground that may limit the establishment of new seedlings.
Botta's pocket gopher is highly adaptable, burrowing into a very diverse array of soils from loose sands to tightly packed clays, and from arid deserts to high altitude meadows. They are able to tolerate such a wide range of soils in part because they dig primarily with their teeth, which are larger and with a thicker layer of enamel than in claw-digging gophers. In comparison, gophers digging with their claws are generally only able to dig in softer soils, because their claws wear down more quickly than teeth do in harder materials.
Botta's pocket gophers are active for a total of about nine hours each day, spending most of their time feeding in their burrows, but are not restricted to either daylight or night time. They make little sound, although they do communicate by making clicking noises, soft hisses, and squeaks.
Their burrows include multiple deep chambers for nesting, food storage, and defecation, that can be as much as 1.6 m (5 ft 3 in) below ground. A series of tunnels close to the surface is used for feeding on plant roots, with shorter side tunnels for disposal of excavated soil. On the surface, the burrows are marked by fan-shaped mounds of excavated soil, with the actual entrance usually kept filled in for protection. Population densities between 10 and 62 per acre have been reported.
Aboveground traces of these burrows are sometimes called "gopher eskers".
Outside of the breeding season, each burrow is inhabited by a single adult, with any young leaving once they are weaned. Male burrows extend over a mean area of 474 m2 (5,100 sq ft), and those of females 286 m2 (3,080 sq ft), but the gophers aggressively defend a larger exclusive area, of 810 m2 (8,700 sq ft) for males and 390 m2 (4,200 sq ft) for females, around the burrow entrance.
The individuals in this gallery are from Pinnacles National Monument, California.