Ridding your garden area of chipmunks is a process requiring multiple steps, and success requires patience. Chipmunks, also called ground squirrels, grow to 10 inches long and are attracted to overgrown, woody areas. The best methods to stop chipmunks from digging holes under flowers include the elimination of the favorable conditions that attracted them to the area, trapping and relocating the animals, and placing a protective barrier around your flowers.
Place the steel trap in an area the chipmunks frequent, preferably at the burrow entrance, and put the bait inside the trap. Acceptable baits include peanut butter, seeds and grains. Do not activate or set the trap. Allow the chipmunk to find the trap and enjoy the bait for a few days. Add additional bait as needed for two to three days. This process increases your chances of success and allows you to capture several chipmunks with a single trap.
Set the trap after the chipmunk has found and enjoyed the bait for a few days. If no chipmunks eat the bait, move the trap to a new location.
Check the trap daily and relocate the trapped animals to a safe and legally acceptable location several miles from your garden. Chipmunks breed twice a year and can have up to eight pups in a single litter, so there is rarely only one animal present. Depending on the severity of the infestation, you may need to continue trapping animals for several days or several weeks. Continue setting the trap until you see no further chipmunk damage, or the trap fails to capture an animal after a week.
Clean the yard thoroughly. Remove leaves and other debris that provide shelter for the pests. Remove bird feeders and any other animal feeders that provide food for the chipmunks. Failure to clean and remove the favorable chipmunk conditions in the the yard will encourage more pests to invade.
Dig an 8-inch-deep ditch around planting beds and line the ditch with 1/4-inch hardware cloth to create an underground fence around the plants. Cover the cloth with soil.
Spread additional hardware cloth over the planting bed to deter digging. Cover the cloth with a thin layer of soil to hide it if desired. Remove the hardware cloth cover during the growing season, or cut holes in the cloth to allow the plants to grow through it.