Chipmunks can really mess up planters and pots by digging in them, as can squirrels. Here are strategies for preventing these cheeky critters from undoing all your efforts:
Use physical deterrents—
Some gardeners fit chicken wire to the surface of the potting soil in their pots. Annuals from six packs are typically small enough to plant directly through the holes of two-inch chicken wire. For larger potted annuals or perennials, it's easy to snip the chicken wire to create larger openings. Secure the chicken wire in place with landscape-fabric pins, because it is light enough for chipmunks and squirrels to fling aside.
For less fuss, try a generous layer of chunky bark mulch or, better yet, river rocks. Bonus: these topdressings will also help the potting mix retain moisture.
Or try what I call the "bed of nails" approach: snip four- to six-inch lengths of twigs or bamboo stakes and insert them throughout the pot. Push them at least halfway down to make them sturdy. It has worked for me!
Use chemical means—
Rodent repellents found at garden centers and hardware stores can be used on and around container plantings, just like in beds and borders. To deter chipmunks and squirrels, try products formulated for rabbits. These can be found as sprays and as granules that can be spread atop the potting mix. Follow the package directions and be ready to reapply.