Thanks for posting your query on Ansys learning forum.
The floquet ports and coupled lattice pair boundaries, would simulate the plane wave effect. You can use these setup and also insert objects at the water/air boundary to see the impact. I don't see any concern in modelling such setup.
From another query, I can understand that you are trying to simulate a parallel plane waveguide setup. If that is the case, you need not have to use PML or radiation boundary assignment. To create a parralel plane waveguide using boundaries, you can assign PEC boundary to the top and bottom face of airbox (along longest dimesion) and PMC boundary to the other side faces of the airbox. For excitation, you can use waveports at other two ends of the airbox where wave is emanating. To create a two different medium, you can insert two separate boxes in airbox and assign respective medium properties. Any intersection error if any, you can override by using options HFSS > Design Settings > Validations > Enable material override.
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