As you see in the last example not the whole scene is modeled with the InnerWorld plug in. The plane simulating the water level is added as an extra object to the scene. After producing the raw mesh you can change its attributes with Blenders 3D tools. For example you can smooth the surface by pressing the "Set Smooth" button in the editing panel.

An other way improving the mesh is subdividing it. For example you create a 64 x 64 mesh with InnerWorld. This should look like a steep coast line. The resulting mesh lacks all this little jagged details. You can improve your mesh with fractal subdivide, a mesh editing tool in Blender.

WARNING: If you make changes in the processing graph or one of the nodes parameters the mesh is recalculated. Any manual refinement work on the mesh done in the 3D view will be lost.