Abstract: Methods to quantify bioburden present in industrial substances are provided that utilize a polymerase chain reaction (PCR) and detection of amplification signals over multiple PCR thermal cycles. The PCR targets a segment of DNA found in one or more biofouling agents that are often found in industrial substances. A sample taken from the substance can be used directly or first filtered, purified, lysed, diluted, or subjected to a combination of such pretreatments. The substance is used in, or is tested for preparedness to be used in, industrial applications and sites, such as non-pharmaceutical applications, non-medical applications, papermaking facilities, leather-treating facilities, and the like. Methods are provided to control or treat substances or systems utilizing such substances, or to control or treat surfaces intended to come into contact with the substances.