The entire water surface belongs to the same brush. It is not in any way cut by the mapper. It is, however, cut by QBSP, into triangles that can be displayed in the engine.

There are several weird cuts in the water surface around that pillar. This could be what upsets your shader. If so, it is rooted in the original map's brushwork.
There are quite simply limits to how much you can do with shaders and textures. Eventually, you would have to solve the underlying problems. That would mean rebuilding the entire set of maps while keeping all this in mind.
Same water and same pillar in RemakeQuake (map rebuilt from scratch):

More regular cuts.
Most of the water in the original e1m2 is ONE BRUSH that runs through the entire map, crossing all walls. The water at the yellow armour is the same brush as the one near the SSG. Only the water at the start is a separate brush, I believe.
Lazy mapping.

There are several weird cuts in the water surface around that pillar. This could be what upsets your shader. If so, it is rooted in the original map's brushwork.
There are quite simply limits to how much you can do with shaders and textures. Eventually, you would have to solve the underlying problems. That would mean rebuilding the entire set of maps while keeping all this in mind.
Same water and same pillar in RemakeQuake (map rebuilt from scratch):

More regular cuts.
Most of the water in the original e1m2 is ONE BRUSH that runs through the entire map, crossing all walls. The water at the yellow armour is the same brush as the one near the SSG. Only the water at the start is a separate brush, I believe.
Lazy mapping.
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