Transparency issue with several objects on top of other transparent objects?

It’s a common problem with transparency, look for “transparency” in this forum. For eg:

In your case, you can make the small blocks always drawn after the water by setting the renderingGroupId property:

https://www.babylonjs-playground.com/#1SLLOJ#1110

You can also have a look at this doc:
https://doc.babylonjs.com/resources/transparency_and_how_meshes_are_rendered

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