The problem of flood protection measures are considered in the paper. The regulation of river flow by the system of Self-Regulated Flood Dams (SRFD) is analyzed. The method of SRFD modeling in GIS environment is proposed. The question of the ecological aspect of the SRFD management is considered based on the hydrophysical properties of the soil. The improved Mualem-Van Genuchted method is proposed for the evaluation of the possible SRFD location influence on the soil of flooded territory - the temporary reservoirs. The importance and utility of the proposed complex method is stated.