That might be possible using Masses. But would possibly generate a solid that would be much much too complex to be worth it.
I would recommend 'faking it' in the sections. Model the Floor using the Pick Lines option in the Sketch environment to generate a footprint that follows the topo closely.
Create a new Floor type that has a negligible thickness with a Glass material applied to it.
In section, all you will see will be a thin line showing the top of the water. That's all you will need. No one will know it isn't a solid except for you. For renderings you can go overboard with applying a Glass material with reflections (again, not recommended unless it's a model meant exclusively for renderings!) and bump maps LOL!!!
Rina Sahay
Autodesk Expert Elite
Revit Architecture Certified Professional
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