Hey Paul. Hard to really know what the proper solution is without some more context/screenshots but here's a few ideas:
* Adjust your rcConfig::ch value to prevent overlapping terrain and water navmesh geometry in those areas
* Build a separate navmesh specifically for water elementals. That would allow Recast to consider water and land polygons together and properly generate navmesh polygons at the area boundaries.
* Prevent recast from generating navmesh data in specific areas by marking them as unworkable in the geometry input step, or remove specific polygons from the final navmesh manually.
Hope that helps.
Graham