Failures of coastal low-lying bridges in the United States along the Gulf Coast have attracted substantial research interest. Many of the failures were associated with twin-deck bridges. This study presents a series of numerical experiments on the characteristics of the periodic wave loads on typical coastal low-lying twin-deck bridges. Firstly, a wave model using the Fourier approximation wave theory is used to represent nonlinear waves generated by a hurricane. The relaxation method is adopted for the numerical wave flume solving the Navier-Stokes (NS) equations in order to minimize the effects of wave reflection. The NS-based model is validated against laboratory measurements with good agreement. The characteristics of wave loads on a prototype coastal bridge with twin decks in the numerical wave flume are systematically studied by considering a variety of gap lengths between the twin decks. The deck gap lengths range from 1 to 40 m, covering the usual values for coastal twin bridges. Both the normalized horizontal and vertical loads on the twin decks under the prescribed conditions are analyzed in detail. Finally, a theoretical analysis of the effects of wave reflection by the landward deck on the characteristics of the wave loads for the twin bridge deck–wave interaction is presented. The results show that the wave loads on the seaward deck are larger than those on the landward deck and both the horizontal and vertical loads on the seaward deck vary as a function of the relative deck gap, the ratio of the deck gap to the wave length. The methodology of the twin bridge deck–wave interaction proposed in the current study can serve as a tool to determine the optimal gap length for a given design wave condition.