Too much water is almost always caused by water geyser, which produce water from nothing. So the main question use it or stop it?
Prevent too much water generation by build a wall all around geysers. The area will fill it with the water and will eventually stop erupting. Insulated tiles are recommended to prevent over heating your base.
If you need more water later, just destroy the wall and water production will resume.
If you are looking for way to use extra water here are several ideas,
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