Odd. I have 2 worlds going at the moment. In one I'm rebuilding 2 villages into a larger villager city. Haven't started tearing down the old, yet, so I'll check the wells to see how the water behaves (or does it?). In the other I gather water from the nearby lake (considered a forest biome, but it's a MASSIVE lake at least 200x200 blocks or larger...haven't fully measured it). Anyway, the water there is 2 blocks deep, but always replenishes correctly.
Not sure what the deal is for you. Have you tried creating a new world to see if it's a global phenomenon or local?