In the deep-water hydrocarbon recovery, the over-pressured sand originating from fast sedimentary compaction brings about difficulties in well control during drilling practices. When encountered by a drill bit, the sand section will generate shallow water flow (SWF) that could substantially jeopardize the integrity of the drill string and the associated equipment, eventually leading to drilling failure. The SWF hazard has been one of the predominant geological hazards in the deep-water drilling operation nowadays. Therefore, it is crucial to accurately identify the SWF hazard, estimate the risk, and take the appropriate measures to minimize the engineering and economic losses. In this study, a set of experimental facility and workflow were proposed, in order to investigate the flow failure behavior of the over-pressured sand section. The experimental findings indicated that the initial overpressure was one of the principal factors of the SWF hazard. Accordingly, a discrete element method-computational fluid dynamics (DEM-CFD) coupling approach and was proposed to model the process of the SWF hazard. The results of the numerical simulation were verified by the behavior of sand transportation disclosed in the laboratory experiment. The simulation showed that the sand production of a specimen increases with three influence factors, including the initial overpressure, the porosity and the sand grain size. Some critical points were discovered and studied in the investigations of each influence factor, and the rising tendency of the curve tended to undergo a dramatic increment at the critical point. Finally, the SWF risk prediction chart was proposed for the fast and convenient identification and evaluation of the SWF risk.