Water will not reformat your code unless you ask it to.
What it will do though, and I think that’s what’s happening here, is consistently use either tabs or spaces (the default is spaces, for Oxygene), so if you have a mixed file (some lines with tabs, some with spaces, it will be saved with all tabs.
You can right-click the file in the Solution tree and choose “Convert to Spaces” to fix the file.
You can’t choose, exactly. If it finds a single tab in the file, it will assume you want tabs, and save with tabs. You can “fix” that to get back to spaces-only with the aforementioned context menu.
If you actually want it mixed (why oh why?) then that is currently not supported (and won’t be. The editor does not have the infrastructure to persist this on a line-by-line basis. But this is not really something anyone should want, anyways…