Coastal protection design heights typically consider the superimposed effects of tides, surges, waves, and relative sea-level rise (SLR), neglecting non-linear feedbacks between these forcing factors. Here, we use hydrodynamic modelling and multivariate statistics to show that shallow coastal areas are extremely sensitive to changing non-linear interactions between individual components caused by SLR. As sea-level increases, the depth-limitation of waves relaxes, resulting in waves with larger periods, greater amplitudes, and higher run-up; moreover, depth and frictional changes affect tide, surge, and wave characteristics, altering the relative importance of other risk factors. Consequently, sea-level driven changes in wave characteristics, and to a lesser extent, tides, amplify the resulting design heights by an average of 48-56%, relative to design changes caused by SLR alone. Since many of the world’s most vulnerable coastlines are impacted by depth-limited waves, our results suggest that the overall influence of SLR may be greatly underestimated in many regions.