I have been having this problem, where 90% of the time, My fort gets water/mud everywhere, even though the Embark claims to have no Aquifer! No matter how many worlds I create, or what biome I embark in, I encounter an Aquifer on the second layer below the surface, and my fort floods(I think it is always salt-water too. Because I cannot designate it as a water source).
And if I dig into a cavern to drain the water, It does drain. But it leaves a small amount (1/7) that Never evaporates. Years have passed, and there is no evaporation.