Take a tip from real world instances when a harbour has been chosen to be built in a geographical location that is not optimal. In many cases, usually because it is a historically chosen site and does not take into consideration modern day common sense and understanding, what engineers have done is build a sea wall to bear the brunt of high tides, tidal bores and storm surges.
So, either:
find a better location for your harbour
build a sea wall sufficiently long and high enough to ensure a placid and consistent surface level in the harbour area behind the sea wall (you could cheat a little here by placing a low capacity water spawner in the harbour area to maintain the surface level)
be god and terraform the sea bed extensively out to sea to reduce the severity of the wavefront - do a little research into how the topology of the sea bed influences the wave behaviour.
-or all of the above
