Gophers dig holes to eat plant roots. Burrowing animals are the prime suspects when a homeowner discovers tunnels and holes in the yard. Many kinds of small animals, such as moles, voles, chipmunks and rats, make holes in the ground.Some, such as moles, create complex tunnel systems, while others, such as rats, dig burrows in which to hide.ther Suspects. Numerous animals dig holes and make tunnels. You may be seeing the work of chipmunks, squirrels, skunks, raccoons or shrews. Snakes also live in ground holes.