The only water-related flower I can think of in botania destroys water source blocks to give mana, there’s nothing (at least off the top of my head) to generate water since getting infinite water is usually a non-issue.
Still, if the drain works infinitely on vanilla water blocks in river biomes then there’s no problem, my base’s pretty high up so all water gets sucked up immediately. What would the correct height interval be for that to happen? I can’t find anything explicit in the changelog, number-wise and checking coverdrain.java doesn’t show a y level that I can easily spot.