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In the present work, the effect of sea level rise (SLR) on blue energy (SGE) in estuaries is investigated for the first time by means of 2D-numerical computation; and the model results are plotted by Ocean Data View (ODV). The Sebou estuary (Morocco) was selected as an example location due to the availability of field survey data and is an optimal site for energy production. To assess the impacts of SLR on salinity gradient energy, three scenarios of sea level rise were used in the model simulation by adding water depths of 0.3 (ΔH-30), 0.6 (ΔH-60), and 0.9 (ΔH-90), combined with freshwater conditions at upstream of the mouth. Firstly, the model was then combined to assess the impact of transport time scales (i.e., Flushing Time (TF) and Residence Time (RT)) due to possible sea-level rise on blue energy in the mouth of the estuary. The results showed that FT for high flow under the present sea-level (0 m) was lower compared to different SLR scenarios (i.e., 0.3 m, 0.6 m, and 0.9 m) and that the FT for low flow under the present sea-level (0 m) was higher compared to different SLR scenarios. The RT for the present sea-level (0 m) and different SLR scenarios was between 14.75 and 33.14h and between 17.11 and 38.92h (0.3m); 21.54–41.23 h (0.6 m); and 27.17–46.27 h (0.9 m), respectively. The increase of salinity gradient energy with residence time and the corresponding decrease with flushing time as a result of the increase in sea level rise is clearly evident in the studied estuarine mouth. For RT the extractable salinity energy increased by 5–17% for SLR values of 0.3 m, 0.6 m, and 0.9 m, respectively. Inversely, the FT decreases the salinity gradient energy for SLR values by 3.4–11%. Secondly, the simulations results for extractable salinity gradient energy showed that the optimal intake points related to the design of a PRO or RED system in the mouth system moves significantly upstream of the estuary in all cases and the maximum zone of optimal intake point may reach >10 km in the worst scenario (ΔH=0.9).