I've had a lot of leather boots over the years, none have ever been water proof like a rubber boot. I think it's probably unreasonable to expect them to be.
I always buy Red Wings, mainly because they come in extremely wide sizes, but they are also very good quality. I usually buy the Gore-Tex lining and it works for a while. The Gore-Tex gives out a lot sooner than the leather boot part, at least in my experience. The GT usually wears out in the areas that do the most bending, right around the top of the sole at the ball of my foot.
I just accept that the best I can expect from a leather boot is "temporary water resistance", not wading, not standing in water, but walk through a puddle or wet grass to to my stand type of water resistance. I put up with that weakness for the comfort of leather, I hate the feel of rubber boots after a while, too sweaty. If I have to wade, I take rubber boots and change into leather at my destination...yeah, it's a pain.