Hi, the excavator copies the water tiles that are next to the ones dug. So if your excavating near shallow water, you'll get shallow water.
At least that is how it's supposed to work. If you're encountering different behavior, please let me know.
I've had multiple requests of somehow being able to toggle between shallow and deep water but I haven't found a clean way to implement that yet.
In any case, thanks for trying my mod and if you have any issue or suggestion don't hesitate to open a thread. But for the next time, please open one in the main mod page instead of the graphics mod ;)