BuildCraft version: 7.99.15 (compat. 7.99.14)
Forge version: 14.23.2.2618
Link to crash report or log: N/A
Singleplayer or multiplayer: Singleplayer
Steps to reproduce: Find flowing water?
Additional information:

It's like it says on the tin. I was as surprised to come to this result as anyone else.

I tried disabling every single one of my other mods. After a couple hours of enabling/disabling mods and testing, I've found only Buildcraft to be the mod I need to enable to cause the issue, and disable to fix the issue.

It's very odd.

Obviously, it could be conflicting with another mod somehow, but I disabled anything even possibly water-related (Smoothwater, OptiFine, FoamFix Anarchy, TexFix, Dynamic Surroundings, Fancy Block Particles, etc) and BC still caused the issue when enabled.

Here's my mod list if it helps. https://pastebin.com/raw/sRZStcKF

BC does not mess with water or rendering in any way so there must be another mod involved as well

try making an instance where you ONLY have BC installed and no other mods, it shoudn't heapen there. Then you can add/remove mods with a binary search (but leaving BC in all the time) to find the other mod that is involved

Unsurprisingly, it is a conflict with Optifine C9. Optifine does have this tendency to break things.

If either Buildcraft or Optifine is enabled, water is fine. But with them both enabled, the rendering for flowing water breaks.

I tried quite a few setting changes in OF, but none seemed to restore flowing water. At least, the ones I could test. A good half of them ended up crashing the game. Bleh.

EDIT: Anisotrophic filtering needs to be on.

So, for clarity:

Buildcraft alone: No issue
Optifine alone: No issue
Optfine with Anisotrophic Filtering on: No issue
Buildcraft + Optfine: No issue
Buildcraft + Optfine with Anisotrophic Filtering: Flowing water is invisible

How does this even happen. Wat.

(Link to optifine issue: sp614x/optifine#1243)

no clue, probably something about BC sprites is somehow making optifine shit itself yet again. you're gona want to report this to optifine to be fixed. Even if it is on their end he should be aware and probably has an idea of what might be causing this

Already reported it to them.

closing as optifine issue and nothing we can fix from our end, see issue above

I think this happens because we depend on the flowing water sprite for the pipe filter (in silicon), and so we replace that sprite (even though vanilla will load it later anyway).

It should be possible to fix this by not loading certain sprites as swappable.

(Obviously that fix won't help for any of the other BC swappable sprites but it's still better than nothing)