The roughness of the 'runways' that I operate from varies with the wind strength, wind direction, tide, currents and boats operating in the vicinity - I am a float plane pilot.
C208's on floats can experience the Concord STC - a drooped nose as a result of the firewall bending from operation in rough water. The maximum demonstrated wave height is 0.6m - not many runways have bumps that high on them. I understand that Cessna has a number of levels of firewall reinforcement to repair / help prevent this problem.
We use a number of techniques to minimize loads on the structure, most importantly looking for the smoothest water, paralleling swells, minimizing high speed operation on the water, use of reverse to stop quickly and flap techniques to get off the water. Some days it just gets too rough to operate - I've heard of pilots jarring their backs in rough water sometimes damaging aircraft and sometimes not.