How do we get rid of chipmunks?
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We do not really have any chipmunks here, so I will tell you of methods that I heard from multiple sources to have worked (and that work on other animals such as squirrels)...
The most effective way to keep them away from plants and certain areas is to fence in these parts of your garden/property. Small mesh, strong netting or wire keeps them away, but of course, it also makes it harder for you to reach these areas.
In regards to natural remedies chipmunks (likewise to squirrels) are said to hate the taste and smell of hot sauce, cayenne and spicy peppers. If you sprinkle or spray that around some of the affected areas (and re-apply it regularly) you can create a certain barrier and prevent them from chewing on sprayed plants.
Supposedly garlic (and marigold) work in similar ways as they are said to have a very potent scent that these little guys cannot stand. However, I also heard that this only works temporarily and sometimes it appears that they start to get used to the scent after a while.
Another solution to repel (not kill!) them is to scatter moth balls around affected areas and holes they might come through. Do not use the mothballs, if you already have chipmunks in your yard as you might deter them from leaving.
If you have a lot of patience and time on your hands, you can also trap the chipmunks (with no-kill traps) and re-locate them several miles away. This would however be rather time consuming but might be a good addition to other solutions...
In any case, I wish you good luck and all the best!
Some ideas on YouTube: https://www.youtube.com/results?search_query=chipmunk+deterrent+natural