As Independent water and power plant projects (IWPPs) connecting electricity generation and desalination is rapidly growing, interest in the SWRO (Seawater reverse osmosis) process is increasing. However, membrane fouling is an important problem in seawater reverse osmosis (SWRO) processes, because it was one of factors by increasing operating expenses. Many studies have been conducted to control this. However, only clean-in-place (CIP) is carried out. There is a need for practical maintenance cleaning. The objective of this study was to examine characteristics of membrane fouling by operating SWRO pilot plants using hot wastewater generated from power plants and derive maintenance chemical cleaning (MCC) applicable to these sites. Results of this study, depending on the operating conditions of the power plant, the influent water temperature showed a change of about 5 degrees C. This affected the operating pressure of the SWRO pilot plant and fluctuates by about be 7 kgf/cm on average. This variation in water temperature caused by characteristics of hot wastewater generated from power plant directly affected fouling on membrane. Results of MCC and cleaning wastewater showed that organic fouling was dominant. With increasing water temperature, the structure of protein was unfolded and its surface charge was converted to positive charge. Such protein with positively charged surface then formed insoluble aggregates through mutual bonding with negative charge of polysaccharide. This was considered the main cause of accelerated membrane fouling. In order to control membrane fouling, possible way of MCC method was derived for field application. It was performed under various conditions (only acid, acid-alkali, alkali-acid, or only alkali). As a result, alkali-acid cleaning was found to be an optimal protocol because the main cause of membrane fouling due to water temperature change was found to be organic foulants. Therefore, it is considered that MCC can be applied as a operational strategy for organic fouling control in a seawater desalination plant using feed water with frequent temperature changes in a power plant.