Note that there are two sides to the pannier war: some people swear by waterproof panniers and others swear at them.
One problem with waterproof panniers is that, as well as they might keep water out, they also equally keep water in (which means packed wet stuff will never dry and get funky).
There are tricks you can use to keep stuff a non-waterproof pannier dry (people mentioned a few).
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Your primary concern is to have a pannier that will hold up. If you have that, don't second guess yourself about waterproof/non-waterproof (for panniers you already own).