What kind of boots are they? Do they have a welt? If they're leather uppers and a rubber sole, with a leather welt in between, then a leather seal allowed to soak in is the best you're going to manage, and make sure you use a sealer on the stitches around the welt (where the sole and the upper connect). Since my boots were used in mountaineering, I used Sno-Seal on them. It works great. You have to let it melt in, usually in a barely warm oven for an hour or more. Don't bake your boots! Welt construction.
If you're talking about another kind of boot, like one made popular by LL Bean, then a different treatment is probably called for. I haven't owned any of these, so can't tell you how to fix a leak in this instance. You would do well to contact the manfacturer of your boots and ask them.