When I first made my base, I put the horizon water fill in the middle. There was nothing in the room to put it on; it was just directly on the floor. The water was quite high, and I raised some of my NPCs that were swimming under the water so that their heads would be above. The nurse never swims, so I left her underwater.
The next time I went to the base, the water level was lower. Barely above the nurse's head. Over time, it got even lower.
I recently put the horizon water fill at the map floor thousands of feet below the base instead. Now there is "smooth water" placed where the horizon water fill was. It was also quite low compared to the nice high water level I had before, but the NPCs were still swimming.
But today when I went into the base, my character could still swim, but the water was so low it wasn't even waist high on the nurse. The inspiration storage treasure chests that used to be half submerged back in the beginning now float above the water.
I haven't moved the NPCs or the inspiration chests since the start, and I only changed the water one time, from horizon fill to a 16x16 plate, and at the time that I changed that, the water level was the same as it had been with the horizon fill, then later continued to fall.
I just tried deleting the water and putting a new water tile, and the water height doesn't change. Hitting undo and redo a few times showed the NPCs changing heights a bit, but the water level doesn't. Inspiration chests still float above the water, crafting stations that used to be deeply submerged are now at the surface, etc.
Does anyone know what is happening? I like the high water level, so I will probably manually raise the water tile relative to the floor, but this is very odd and I hope it doesn't keep dropping.
UPDATE:
I ran some tests, which you can find detailed more on page 2. A few highlights:
-'fill' type water places the water 1 foot higher than the water surface tiles.
-PCs swim at different heights to match the water when out of the editor, but in the editor, they swim at the same height in both, placing small characters noticably underwater while swimming in the fill tiles while editing.
-This doesn't account for all the odd behavior I saw. For example, I had players that visited the base during lulls in the Mapserver event comment in surprise that they were swimming underwater. In my tests, this only happened while editing.
- The extra weirdness may just be due to the Mapserver April Fools event, where quite a few things were behaving weirdly.