The water physics engine needs a touch up. I had a massive natural reservoir of contaminated water. I created a reservoir closer to my base, and wanted to use gravity to allow the water to flow into it. The water had to flow down several slopes and along small segments of flat ground. The result was ankle-deep water on each flat surface. What should have been too much water for my reservoir to contain, ended up being not even enough to submerge a pump.
Simply had a setup as detailed in the attached image, and dug out a few tiles from beneath the initial natural water reservoir in order to allow it to flow.