For safety and survival at sea and on the shore, wave predictions are essential for marine-related activities, such as harbor operations, naval navigation, and other coastal and offshore activities. In general, wave height predictions rely heavily on numerical simulations. The computational cost of such a simulation can be very high (and it can be time-consuming), especially when considering a complex coastal area, since these simulations require high-resolution grids. This study utilized a deep learning technique called bidirectional long short-term memory (BiLSTM) for wave forecasting to save computing time and to produce accurate predictions. The deep learning method was trained using wave data obtained by a continuous numerical wave simulation using the SWAN wave model over a 20-year period with ECMWF ERA-5 wind data. We utilized highly spatially correlated wind as input for the deep learning method to select the best feature for wave forecasting. We chose an area with a complex geometry as the study case, an area in Indonesia’s Java Sea. We also compared the results of wave prediction using BiLSTM with those of other methods, i.e., LSTM, support vector regression (SVR), and a generalized regression neural network (GRNN). The forecasting results using the BiLSTM were the best, with a correlation coefficient of 0.96 and an RMSE value of 0.06.