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There is some stuff called shoe goo that works pretty well. it's basically silicone I think, but it's more adhesive, so it'll waterproof and stay stuck where you put it better. If you can force it into the crack, that'll work better then smearing it on the outside.
go to Basspro shop, dicks or any other outdoor store you have in your area. get some shoes that have a "goretex" liner in them, they are completely waterproof unless you wear out the lining in them.
I have a pair of goretex boots, however, those are my hunting boots and not my work boots. I'm just looking for a cheap fix so I can still walk through puddles.