skunks are digging in your garden because there is food there, skunks favorite snack are the grubs that live in your soil. so in a way they are doing you a favor, they are telling you,... "hey, you have grubs in your lawn" you can do one of two things. 1. get rid of the grubs, apply grub killer, they are going for the white grubs that mature into a Japanese beetle, they will keep digging through your soil until they dont find anymore little goodies there. grub killers are in every yard and garden section of your stores. 2. Fence them out, a 3 foot high chicken wire fence with about 6 inches buried in the ground will keep them out. they dont like to climb so they wont go up the fence but they like to dig so you need to have it buried some.