A recent change to MT 5.1.0-dev.
Any liquid nodes you want to be affected by the waving water shader will need 'waving = 3,' added to the node definition. There was no way to make this compatible so mods and games will need updating.
Previously, when the waving water shader was enabled, all liquid nodes waved, there was no use of 'waving = 1' in nodedefs as used by the waving leaves and waving plants shaders.
Now, waving water is consistent with the other waving shaders. 'waving = 3' is required in a nodedef to allow a liquid node to wave when the client enables the waving water shader.
Meshes and nodeboxes can also use 'waving = 3' to ripple vertically.
Issue https://github.com/minetest/minetest/issues/5694
Engine PR https://github.com/minetest/minetest/pull/8418
MTG PR https://github.com/minetest/minetest_game/pull/2346