This study presents the assessment and seasonal variation of wave energy along the southern coast of Java, Bali, and Nusa Tenggara Waters. For this purpose, the WAVEWATCH-III numerical model was used to simulate the Significant Wave Height in the study region over 25 years covering the time interval of 1991–2015. Wind field data input for the model was a combined dataset of Cross-Calibrated Multi-Platform, Navy Global Environmental Model, and Navy Operational Global Atmospheric Prediction System. In general, the simulation results showed that there was a good potential of wave energy along the southern coast of Java and Bali with the value of higher than 20 kW/m. Furthermore, it was found that there were 12 points which were considered to be the most promising high wave energy potential spots along the near-shore coastal waters of the Java and Bali southern coast. There was a noticeable seasonal variation of wave energy along the study area associated with tropical monsoon climates, which led to the highest value in the period of June to August for about 40 kW/m and the lowest value in the period of December to February for about 20 kW/m. All the selected points for wave energy exhibited dominant wave propagation between northward and northeastward. Moreover, there was an evident increasing trend of wave energy with the peak value appearing in 2005 for all stations.

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