Projections of potential submerged area due to sea level rise are helpful for improving understanding of the influence of ongoing global warming on coastal areas. The Ensemble Empirical Mode Decomposition method is used to adaptively decompose the sea level time series in order to extract the secular trend component. Then the linear relationship between the global mean sea level (GMSL) change and the Zhujiang (Pearl) River Delta (PRD) sea level change is calculated: an increase of 1.0 m in the GMSL corresponds to a 1.3 m (uncertainty interval from 1.25 to 1.46 m) increase in the PRD. Based on this relationship and the GMSL rise projected by the Coupled Model Intercomparison Project Phase 5 under three greenhouse gas emission scenarios (representative concentration pathways, or RCPs, from low to high emission scenarios RCP2.6, RCP4.5, and RCP8.5), the PRD sea level is calculated and projected for the period 2006–2100. By around the year 2050, the PRD sea level will rise 0.29 (0.21 to 0.40) m under RCP2.6, 0.31 (0.22 to 0.42) m under RCP4.5, and 0.34 (0.25 to 0.46) m under RCP8.5, respectively. By 2100, it will rise 0.59 (0.36 to 0.88) m, 0.71 (0.47 to 1.02) m, and 1.0 (0.68 to 1.41) m, respectively. In addition, considering the extreme value of relative sea level due to land subsidence (i.e., 0.20 m) and that obtained from intermonthly variability (i.e., 0.33 m), the PRD sea level will rise 1.94 m by the year 2100 under the RCP8.5 scenario with the upper uncertainty level (i.e., 1.41 m). Accordingly, the potential submerged area is 8.57×103 km2 for the PRD, about 1.3 times its present area.