As reported extensively in both electronic and print media in Indonesia, high wave and anomalously high sea level phenomena occurred in February 2008 in Indonesian waters, mainly along the western coast of Sumatra and the southern coasts of Java-Bali. Tropical Cyclone (TC) Nicholas, occurring in northwestern coastal waters of Australia between 11 and 20 February 2008, might have contributed to the existence of these phenomena in the Indonesian region. This study focused on investigating the effect of TC Nicholas on the increases in sea levels in the Indonesian waters by analyzing residual water levels (non-astronomic tide). In this regard, a storm tide event (the sum of the astronomical tide and storm surge generated by the TC Nicholas) was simulated in this region using the Regional Ocean Modeling System (ROMS). The residual water levels were obtained by removing the tidal part (astronomic tide) from the ROMS simulated total water levels. In addition, to confirm possible influences of TC Nicholas, a lagged correlation analysis was applied between atmospheric pressure at the center of TC Nicholas and residual water level oscillations in the Indonesian waters. It was found that the residual water levels showed a strong correlation with the atmospheric pressure at the center of TC Nicholas in some areas of the Indonesian seas, such as the western coast of Sumatra, the southern coast of Java, Lesser Sunda Islands, and the southern coast of Papua. The increased sea levels on the western coast of Sumatra are up to 16 cm, with TC Nicholas leading the residual water level by 4.18 days (TL: time lag). Meanwhile, they are up to 20 cm (TL = 5.75 days), 21 cm (TL = 1.12 days), and 38 cm (TL = 3.96 days) on the southern coast of Java, the Lesser Sunda Islands, and the southern coast of Papua, respectively. The results of this study could be used as an initial assessment to investigate the most vulnerable Indonesian coastal areas to the impact of the TC and they might be significantly beneficial for designing both a proper disaster risk reduction program and investment policies in the region, particularly in the context of flood risk reduction and adaptation.