Glass seems to be completely invisible when seen from below the water's surface.
This does not occur when vanilla-like water is toggled on, but that kinda defeats part of the point of using a shaderpack for me.

Absolutely love this shader otherwise.

Damn, well that's all good. If it's a hard limit then so be it.

I will just use it on vanilla like and use a resource pack to make it look the best I can. Thanks for the quick response.

I'm sorry. This is expected behavior due to the way water has been implemented. You can't see any translucent objects through it. I know in other shaders it's possible to see them, but it's always at the cost of something else. For example, the opposite usually happens: it's the water that wouldn't be rendered correctly through translucent objects. It's typically one or the other. Some people manage to solve it, but again, it's always at the cost of something. These are inherent limitations of the shader mod.

On the other hand, if you use clear glass, it should be visible, if I'm correct. The issue is only with colored glass, and in general, any translucent object. Those objects are rendered in a different pass.