Bad water has to be better than NO water�..right?
I have no well, and have a contingency plan similar to yours. So I know exactly what you're facing.
If the water will keep your fish alive, it seems you have no choice. Wait until the last minute. I hope you get rain, and it isn't necessary.
If you are forced to use the overly-fertile water, chances are, you will get plenty of rain this fall and the water will return to normal.
Good luck!