The present invention provides a method of operating a reprocessor that has a chamber for receiving items to be sterilized. The reprocessor is filled with water that has passed through a first and a second filter element that both comprise a filtration system. A liquid sterilant is generated by mixing the water with dry chemical reagents. The liquid sterilant is circulated through a fluid circulation system and the filtration system wherein a portion of the liquid sterilant is directed through a bypass conduit and another portion is directed through the first and second filter elements. After a predetermined exposure time, the reprocessor is drained. Then the reprocessor is filled with water for rinsing that has passed through the first and the second filter elements. The water for rinsing is heated prior to being introduced into the reprocessor.