Urban sewer systems has a limitation of capacity of rainwater storage and problem of occurrence of untreated sewage, so adopting a storage facility for sewer flooding prevention and urban non-point pollution reduction has a big attention. The Korea Ministry of Environment has recently introduced a new concept of "multi-functional storage facility", which is crucial not only in preventive stormwater management but also in dealing with combined sewer overflow and sanitary sewer discharge, and also has been promoting its adoption. However, reserving a space for a single large-scale storage facility might be difficult especially in urban areas. Thus, decentralized construction of small- and midium-sized storage facilities and its operation have been introduced as an alternative way. In this paper, we propose a model predictive control scheme for an optimized operation of distributed storage facilities and sewer networks. To this aim, we first describe the mathematical model of each component of networks system which enables us to analyze its detailed dynamic behavior. Second, overflow locations and volumes will be predicted based on the developed network model with data on the external inflow occurred at specific locations of the network. MPC scheme based on the introduced particle swarm optimization technique then produces the optimized the gate setting for sewer network flow control, which minimizes sewer flooding and maximizes the potential storage capacity. Finally, the operational efficacy of the proposed control scheme is demonstrated by simulation study with virtual rainstorm event.