Mold needs nutrients and moisture to grow. Therefore, reducing those two components in the arena floor will reduce mold growth. To reduce moisture, the airflow inside the barn needs to be adequate — typically a minimum of four to eight air changes per hour through natural ventilation in from the eaves and out through the top ridge vents or cupolas. Don't keep the barn airtight by closing eaves and roof ridges, or the air will quickly become saturated with water vapor. Sometimes forced air ventilation using fans may be needed, depending on the barn design.
Including something in the arena floor that absorbs moisture may help, too. Calcium chloride (ice melt) incorporated into the flooring may help some, but it alone may not be able to overcome a total lack of ventilation.
Removing high-nutrient soil that has a lot of fine dirt and manure and replacing it with low organic-matter sand will reduce the substrates that mold can use for nutrients.
