I think your options are to try some sort of motion-detector spray that you hook up to your hose, or to trap them with a live or snap trap. See this discussion from another Hometalk member who faced the same problem:
I tried the motion detector spray on deer, I think with the amount of chipmunks I have my garden would be overwatered! Thank you for the suggestion.
The mothballs have helped alot this year, I will try your other suggestions. Does anyone know of a PLANT or HERB that might help?
Hi Audrey, I did a quick search and "no", there is no "natural" way to help with chipmunks. As Douglas said the best option is trapping. The only other thig mentioned was keepng your yard free of piles of stone or twigs where they may be staying will also help.
That really is not an option for us, my husband has created stone walls, all over our property. The chipmunks living in the stone walls moved when I litered the areas with the moth balls. I know that the moth balls did work tremendous amount this year, I know the smell works also on detering deer, I will have to try to find very fragrant herbs or flowers to plant. Thanks you all for your help!
Thank you for all your comments and suggestions, I think we will have to handle this with aromatic herbs, cayenne pepper spray and lots of moth balls. Thanks again for all your help!