© Springer International Publishing AG 2016. System analysis of network of flows of water is essential for assessing risk of flooding. The flood risk management generally focuses on the meteorological forecasting together with the operation of hydraulic structure while overlooks the flood incurred by inefficient performance of natural instrument in flood mitigation, namely of canal systems. A new methodology for the risk assessment of flood from the prospect of the capacity of canal system is proposed in this paper. The methodology comprises the modeling of a canal system by a flow network in the graph theory, the formulation for the determination of the system capacity in terms of the maximum flow problem, the treatment of uncertainty using copula couple with maximum entropy models, the definition of flood risk event, and the method of risk assessment. The application of the proposed methodology is illustrated through a numerical example.