Perhaps your shader has been modified to add opacity with Distance to Nearest Surface?
If that isn’t the case, try to replicate this in a new project and provide steps for replication…
I apologize for my English, as I am not very proficient in it. It will be quite difficult to translate your message accurately, but I’ll do my best to convey the meaning. From what I understood, you mentioned a project involving a map and various elements. You mentioned that when you tried to do it on a flat surface, it seemed fine. However, when you used a real-world terrain displacement map and made some adjustments, the parameters might not have been proportional, resulting in a landscape with square bumps that you later smoothed out with tools. Could this be the reason? And you also mentioned that after adding rivers using a water plugin, a certain issue occurs over time.
