A water flow rendered by the current Sodium next branch:

The same water flow, rendered in vanilla:

I'm not sure if this is intended behavior or not.

I made a PR to fix this issue with #2467. Does it work as expected?

yes it does.

This issue is still valid in 0.4.10. The difference is really hard to see though.

this is a duplicate of #38, it’s a translucency sorting issue. the fix is non-trivial, but the dev team is working on it.

I've got similar issues with my water as well. However, I've got an issue where water makes ice transparent for whatever reason.

The original report is not #38, but the followup images are.

As coderbot mentioned, the orientation of the crease is changed. I've discovered that the orientation of the crease is differs between the inside-facing and outside-facing quad of such a piece of water. I've attached two screenshots from within and outside of water with the crease highlighted.

Not sure if this is the correct place to post this, but I have had some other weird issues with water that seem similar to what your are having:

@mscatloaf The problem you are showing here is #38. This issue is about the particular shape of the water flow, not the translucency problems when they overlap.

This is #38 - lack of translucency sorting - right?

That's what I originally thought, however if you look closely at the top of the water flow, you can see that the geometry of the diagonal faces is quite different (a flat face instead of a "V" face). It seems like this is separate from the previous translucency sorting issues.

It's possible that this is actually related to the fact that vanilla is generating degenerate non-coplanar quads here, and since Sodium changes the orientation of vertices in quads due to lighting, it might be changing the appearance of the quads too.

A non-coplanar quad will render differently depending on how it is converted to triangles, and changing the orientation of the vertices changes how it is converted to triangles: