During the summer, I plant vegetables in containers and keep them on my deck. In the past, I've had a great deal of difficulty keeping the squirrels from digging up my new sprouts. A friend gave me an idea which has worked well. What you do is get a package of bamboo skewers, which usually runs about a dollar, and stick the skewers into the soil, with the points sticking up out of the soil and over the edge of the pot.
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I have lost hundreds of dollars and many man hours due to squirrels digging in potted plants. I would come home from work only to find many pots knocked off a wall or bench.
Don't bother with the tip about scattering moth balls. I did this and next morning, they were all GONE. The squirrels must have loved them.
Squirrels love to hide their food. In the process of doing this, they tend to bury the food in soft dirt which is usually a newly planted garden.
If you have pets or animals that roam your area try adding chicken wire under your plants.
You may want to keep squirrels out of your garden or bird feeders. This is a page about natural repellent for squirrels.
As cute as they may be squirrels can also make themselves into pests and lose their welcome in your garden. This is a page about squirrels eating flowers.