This study examines the impact of climate change on wave overtopping discharge (q) at eight Moroccan Mediterranean ports, under climate scenarios SSP2-4.5 and SSP5-8.5, projected to the year 2100. To address inter-model variability and better represent future conditions, wave data from four different models were used. The analysis considers three return periods—1, 5, and 25 years—and includes both central estimates and values from the 90% confidence intervals to assess uncertainty from sea level rise (SLR) and wave projections. Results show that overtopping discharges increase with return period, along with the number of ports affected. At 1 year, two ports exceed tolerable thresholds; at 5 years, three ports are impacted; and at 25 years, nearly all ports face overtopping risks. When varying SLR while holding wave height (Hs) constant, discharge variations remain within one order of magnitude. However, when varying Hs with constant SLR, variations span two to three orders of magnitude. These results suggest that accurate Hs projections are more critical than SLR in estimating overtopping risk, emphasizing the need to reduce wave forecast uncertainty to support climate adaptation strategies.