Characteristics of the operation and management of irrigation systems were analyzed in the low lying paddy area with creek networks. The irrigation system in Kubota district was chosen as a suitable example for analyzing. The water use in the irrigation system is characterized by reuse of return flow from paddy fields to creeks utilizing those water storage functions. There is a time delay between the input water and run off in the creek network irrigation system. The complex tank model was, therefore, applied to analyze the system operation. It is clarified that the response of actual operation of the irrigation system due to rainfall depends on the drainage conditions affected by tidal phenomena of each block.