To provide a method for judging the cause of clogging in a water-treating installation by which a precise clogging-preventing countermeasure is applied by judging whether the cause of the clogging of the water-treating installation is microorganisms or not and identifying the kind when the cause is the microorganisms.

The method for judging the cause of the clogging of the water-treating installation comprises extracting a DNA from an attachment to a device in the water-treating installation, replicating a specific site of the DNA chain by a PCR, and estimating the number of the microorganisms attached to the device from the replicated number.