So sometimes when i walk in very low areas in TR, i see water mixed in with ground textures. kind of like the water level is interfering with the ground textures. Is there a fix for this? It is kinda distracting.

Are you perhaps talking about TR's lower-resolution unique water meshes? From what I remember they use these because Morrowind is coded to have water at a fixed level so in order to have like ponds in the hills, they have to use unique meshes and textures and TR's textures are built to be compatible with the vanilla game so they are lower-resolution.

EDIT: I seem to recall that on the Nexus there is a mod to make the textures a bit better.

Could you specify which areas? And what wave height do you currently use? I know that a certain area near Dreynim in our Sacred East release had some bits of landscape that was just barely above water level, meaning any wave height > vanilla standard might get the result you're describing. If this is the case, please give me an example of where and I'll have it fixed by our next update.