Why is it recommended to not operate the ionization system if the alkalinity is below 100?

This is due to the relationship of Alkalinity and copper.  Copper ions can be more toxic to fish if the alkalinity is below 50.  A good range of alkalinity level is between 100-180 mg/L (ppm).  A maximum suggested range is between 100 – 250 mg/L (ppm).  One easy way to raise low alkalinity is to use ordinary baking soda.  Adding ¼ cup (0.15 lbs) per 1,000 gallons will typically raise the alkalinity by 10 mg/L (ppm).  Raising the alkalinity should not be done all at once, but over a period of days.