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Africa's coastal regions, already burdened by accelerating sea level rise, faced unprecedented threats from the 2023–2024 El Niño, which triggered record surges across marine domains while compounding a long-term regional increase of 11.26 cm since 1993. Here we analyze high-resolution satellite altimetry from 1993 to 2024. Our analysis reveals how anomalous winds suppressed coastal upwelling, sparking marine heatwaves. This drove a record upper-ocean heat buildup, quadrupling prior maxima, and produced a regional surge of 8.39 cm. Steric effects accounted for over 80% of the rise in the Atlantic and Indian Oceans, with thermal expansion dominating the steric signal, while in the Mediterranean, ocean mass changes played a nearly equal role. Thermal expansion was the overwhelming driver, with steric effects accounting for over 80% of the rise in the Atlantic and Indian Oceans, while in the Mediterranean, ocean mass changes played a nearly equal role. Critically, this event’s disproportionate impact demonstrates nonlinear amplification. Record ocean stratification, more than double that of previous super El Niños, trapped surface heat, intensifying the steric response. This is magnified by a post-2008 regime shift that increased sea level trends by 71%. Consequently, El Niño events now explain 24.7% of interannual variability, underscoring their growing dominance. This dynamic creates a compound threat for Africa’s vulnerable coasts: extreme flood risks from sea level rise and land subsidence (>3 mm/year) are coupled with collapsing marine productivity, demanding urgent adaptation in low-lying deltas and Small Island Developing States.