Only a minor comment: There is no such thing like a freshwater estuary. The sea always moves its salt water into the estuary at the bottom during floods. Exceptions are very mighty rivers lke Amazonas. Do to horizontally varying saltwater intrusions into estuaries you can also get strong fronts which you really see at the surface in form of local wave intensity. Kayakists know that phenomenon very well...
Indeed longer fetch and duration of steady wind in the open ocean in comparison to in an enclosed bay is the most significant reason of higher wave activity. Viscosity plays a negligible role in gravity wave generation. Also, in the presence of swell, wind wave generation tends to be most efficient, also contributing to higher waves in open water than in enclosed regions.
In addition to the role of a longer fetch and stronger winds in the open ocean, a semi-enclosed bay is sheltered from swell from most directions, which reduce the occurrence of large waves
For a given Fetch and a given duration of wind, the wave generated by the wind in a great lake (fresh water) can be as sharp and as high as the waves generated in sea (salt waters). ( see different M. Donelan papers in JPO or JGR).
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