It works using a high res DTM in WMTS for all France. Antoine Masse ([hidden email]) worked on it with a higher resolution DTM (created from lidar to classic grid WMTS) for french littoral also. You can specify your DTM in the WMTS_Provider.js (it's better in the last versions as you specify it in the index.html/JSON)
Then the flood was computed in the globe shaders changing the rendering depending on water depth. Another technic is to create a physical mesh for the water.
Chargé d'Etudes et de Recherche
Laboratoire MATIS, IGN
Tel: 01 43 98 85 73