Many studies on membrane fouling have been made and reported, and it has been revealed, based on liquid chromatography organic carbon detection (LC-OCD), that biopolymer is the main foulant in the drinking water treatment process, in which the raw water is taken from a river or a dam. However, measurement by LC-OCD is time-consuming and costly. Therefore, continuous measurement of biopolymer concentration by LC-OCD is not feasible. For this reason, we have not been able to monitor biopolymer continuously and control membrane fouling. The purpose of this study is to find a new fouling index (FR) to control membrane fouling without measuring the biopolymer concentration. Then, we tried to find a correlation between biopolymer and other water components by a multiple regression analysis. As the result, we have suggested the new fouling index (FR) which consists of the sum of the fluorescence intensity within the Region III domain measured by excitation emission matrix (EEM) fluorescence spectroscopy and the concentration of dissolved organic carbon measured by the total organic carbon (TOC) measurement. TOC and EEM are measured easily and continuously. Thus, we can control membrane fouling by monitoring the FR continuously.