Gophers, prairie dogs, and other mammal pests can indeed damage fruit trees, garden vegetables, and agricultural crops. In addition to damaging plants, gophers may burrow into levees and ditches damaging irrigation systems, harvesting equipment, utility cables, and can cause enhanced soil loss by erosion.
According to the National Center for Appropriate Technology, Alfalfa provides a very desirable habitat for several mammal pests that include mice, gophers, ground squirrels, and rabbits. Proper identification of the species involved is critical, because control measures differ with each one. Assistance in correctly identifying the animals causing the damage is available through the local Extension service.
Field Mice (Mictotus spp), also called meadow voles, dig short, shallow burrows and make underground nests, creating trails about two inches wide that lead from their burrows to surrounding areas of the field where they feed. Control measures consist of cutting the surrounding vegetation in ditches and adjacent fields, trapping (which can be impractical when populations are high), the use of ammonium-based repellents (check with certifier), and habitat creation for raptors and mammal predators such as coyotes, foxes, wildcats, weasels, and shrews.
Gophers (Thomomys spp.) are burrowing rodents that feed mostly on underground plant parts, with alfalfa being one of their preferred foods. Besides weakening or killing the plants, they also damage irrigation ditches and borders. The mounds of soil they push up from their burrows also bury other plants and cause obstacles for the harvesting equipment. Non-toxic controls consist of trapping, flooding the burrows, surrounding a field with plants that repel gophers, such as gopher spurge (Euphorbia lathyrus) and castor bean (Ricinus communis). Depositing predator urine, pine oil, or any other foul smelling substances in the burrows has been reported to provide temporary control. The use of barn owl perches to attract these predators has been successful in controlling gophers in California. On average, a barn owl can eat 155 gophers per year (Power, 2003). Propane devices that ignite injected gas, causing the burrows to explode, are reported effective in reducing populations temporarily. Check with your certifier before using this method. Additional treatments are necessary, depending on the length of the season.
Control measures include trapping, baits and fumigants. Some of the baits and fumigants are restricted and not available to homeowners. Professional pest control companies are beneficial in this case. Exclusion by “fencing” root systems of landscape plants as protection from gophers is recommended, but this should be done with caution. The hardware cloth recommended for this purpose can girdle tree and shrub roots, resulting in plant death if installed too close to the plant. The appropriate distance to install hardware cloth from the plant will depend on specific plant root systems. Lining the base of raised planter beds with hardware cloth can help protect vegetable and flower gardens.
Some plants may be advertised as gopher repellent plants, but these are just plants that the gophers will avoid, going around or under them to get to desired plants. At least these are plants that gophers will usually not damage; however, some of these plants have their own negative characteristics, such as causing dermatitis in humans.
A good place to look for control information is NMSU Extension Publication, L-109, Controlling Pocket Gophers in New Mexico (http://aces.nmsu.edu/pubs/_l/L109.pdf).
https://attra.ncat.org/attra-pub/alfalfa/alfalfa_vertebrate_pests.html
https://attra.ncat.org/calendar/question.php/how_can_i_control_rodents_organically
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