It is difficult to discourage pocket gophers from yards and gardens when we provide such a banquet for them there. Repellents, noise/vibration makers, and most other commercial products have not been proven to be effective. This is why trapping, fumigation, and poisons are so often used and recommended for control. You can try flooding the holes, but don't expect great results. For protection of prized gardens and landscape plants, it may be necessary to install an underground fence of 1/4- to 1/2-inch wire mesh at least 36 inches below the soil surface. The sandier your soil, the deeper the gophers will burrow, so keep that in mind. In fact, research on Botta pocket gophers indicates that they will burrow below 5 feet (marked gophers in these underground enclosures were found in adjoining enclosures).

Gophers do not hibernate and can continue to cause damage throughout the winter. Caging or boxtrapping of gophers is not really humane; moving the animal (after gaining permission to relocate it to someone else's property) almost always results in death of the animal. Gophers are very, very territorial. If you do decide to resort to harsher control methods, these are best done in the fall and spring.

Here is a good reference from the University of Nebraska that provides more information on pocket gopher control:
http://www.ianr.unl.edu/pubs/wildlife/g1290.htm#CONTDAM