Screenshots 2 and 3 look like a map that were QBSP'ed and VIS'ed without transparent water support - the vis data is culling stuff beneath the water surface when the player is above, because it thinks you can't see under the surface, but the engine is using transparency so you can see through and it looks glitchy.

The fix is to run QBSP with transparent water support. I'm not sure which tools you are using but check the docs for a "-transwater" command or something like ythat. If your tools don't have it my quake compiling suite does by default: http://ericwa.github.io/ericw-tools/ ; it supports hexen 2 with the -hexen2 flag added to qbsp.

but I slowly 'chunked off' entire parts of the map with giant wall chunks, and deleting any lights, etc that would've been outside the map, to try and find where the leak was.
This works but there are easier ways; TrenchBroom and JACK can load the pts file which should draw a path that goes through the leak. I think you can also load the leak in the engine with the "pointfile" command (in Quake at least). 

"I'm not sure which tools you are using but check the docs for a "-transwater" command or something like ythat. If your tools don't have it my quake compiling suite does by default: http://ericwa.github.io/ericw-tools/ ; it supports hexen 2 with the -hexen2 flag added to qbsp. "

To be honest, I'm not sure. I'm using that editor called BSP and - I had used it before long ago on my old computer, but when I tried to install it more recently on my new computer, I had forgotten how I got it all set up to actually work (error messages, missing files etc), and couldn't get it to run. So I just copied the entire folder over from my old computer on a flash drive. The point being that I'm not sure if the compile tools were downloaded separately or what, can't remember, but they are Bat files called Fast.bat, Full.bat, Leaktest.bat, Novis.bat, Relight.bat, Super.bat. I only have a general idea of how it all works and I usually just run Full.bat and then copy the created .bsp to my H2 folder to test it ingame.

The weird thing about the compiler not supporting transparent water is that...well... it WAS, before. I have no idea why it isn't now. In fact, "r_transwater" isn't even a valid command in the H2 console, and I'm unsure of where I could've accidentally turned off a setting like this, since the build files are just Bats that I run from a drop-down from the editor. :[

The easiest thing for me to try first (I only thought of this now), is to re-copy over my BSP editor files, so I'll try that first. 

I suggest using Necros' compiler GUI and Ericw's tools instead of those batch files that came with BSP. You will just have Nercos' GUI running in the background and alt tab to it when you want to compile.

The GUI is the easiest way to compile maps and it's extremely customizable. I recommend reading the entire web page before using it:

https://shoresofnis.wordpress.com/utilities/ne_q1spcompilinggui/ 

GUI program wants these. I have them, but nowhere that I put them it seems to like?

I tried:

same directory as Compiling GUI
directory of .map file (source)
directory of .bsp (output)
directory of the utils (qbsp, vis, light)
system32
sysWOW64

(I needed these dlls before for using bsputil, but putting them in the same folder as bsputil solved that) 

Disregard that, sorry. This was a problem of 32- 64- mismatching. The DLLs I have mentioned in the above post, are 32-bit, because other tools that required them were 32-bit. My OS is 64 so I downloaded 64-bit of eric's tools, thus it didn't recognize the DLLs existing. Whoops. :) 

..And for some good news..

https://i.imgur.com/qX21b3a.png

The water transparency is correct again now! The GUI+eric's compilers worked out

Thanks, guys.
I KNEW there wasn't a leak, man!

I have no idea why transparency suddenly disabled itself in the pre-packaged qbsp.exe/vis.exe/light.exe that came with my "BSP" Editor, and I will probably never find out either. The next thing is probably to download Hammer of Thyrion but I think I'll work on the map for a while first. :) 

Glad you got it working. take a look at *waterskip in the qbsp readme of eric's tools. if you put that texture on every surface but the top of the water - it really helps with weird water effects. 

Hmm, I used TexMex to add a *WATERSKIP texture to my wad and put it on all the water brush surfaces, aside from the top surfaces - but I still get the wavy vertices for any underwater geometry. Maybe a Hexen 2 specific problem? Or is there something else I need to do?

They worked, though, in the sense that it was still water in-game, and they were invisible - that is, the sides of adjacent water brushes were invisible - but they were actually invisible before, also. 

The "wavy" water is a in-engine feature. Not related to textures. 

My bad, what did you mean earlier with weird water effects being addressed with *waterskip? 

Bad choice of words on my part. What I should have said is that *waterskip can make using water easier and cleaner overall. When you jump in a pool of water you should not see the boundary of the brushes under water. A lot of mappers avoid this by making the brush bigger. Bust sometimes you cannot do this. Much easier and cleaner to use the skip workaround. 

To tell you the truth, I was expecting what you say to happen - originally - when I built my map for the first time. Since I had used the same water texture for all sides of the water brushes, I had wondered if those side faces would be visible in-game. (I do indeed have adjacent water brushes)

It turns out those faces weren't visible though, and the water looked normal (normal aside from the translating vertex effect) - though I'd imagine this may be something dependent on the compiler used (?)

Good habit though. I remember using a "CAULK" texture for basically every brush surface, other than the visible ones, when I was making a map for Return to Castle Wolfenstein in Radiant. 

Anybody know where I can find custom monsters and weapons for Quake 1? I googled it but the only links I found where dead. 

it is your main bet. Go to Quaddicted, search for the ''weapons'' or ''monsters'' tags and when you have found some that you like ask the author if they can be freely used or not.

Apart from the big mods there is only a handful with more than two or three enemies or any new weapon. 

idgames2 archive will have lots of custom mods and weapons...

Quaddicted is one of the few places that it still exists.

https://www.quaddicted.com/files/idgames2/ 

Checkout the Keep mod. It has a very very large amount of custom monsters because I've added in enemies from mods all across the Quake community. Code qc source is provided if you want any particular enemies.

http://celephais.net/board/view_thread.php?id=61506&start=212 

I have some textures I want to use in Quake but they are in png format and not in a wad file. I used slade to create a wad file out of them but I just got an error when loading the wad in trenchbroom.

If I have png images I want to turn into usable textures how do I do this? I play my maps in quakespasm or darkplaces so I don't care about vanilla compatibility. 

make sure you wrote a WAD2(quake) and not a WAD3(halflife).

also note that quake's textures are tiny. a high-res png dumped into a wad will be a pain to map with, assuming your editor doesn't reject the 'excessive' size.
remember: 1qu = 1 texel.
(engines will repeat replacement textures on the same boundaries as the low res textures, so if you set up the size of your wad images to be the default size for your texture in quake units then you won't need to rescale images or deal with the lightmap seems that can result from that.)

and make sure that your wad images don't end up with undesired random fullbrights, because those suck. 

I am not using very large textures. I am using these: https://www.doomworld.com/forum/topic/92309-doom-3-textures-for-doom/

Originally they were intended for Doom but I figured I could use them for Quake as well.

And how do I safe a as wad2 instead of a normal wad? When I choose "safe as" I only get the option to safe as a wad file and don't see any other alternative. I am using Slade3. 

You can find wad files with those textures already made for q1 at Quaddicted:

https://www.quaddicted.com/files/wads/

hth 

thanks for that mate! 

Hey, newbie in custom mapping
Trying to test my first quake2 test map .bsp and I get this error when launching KMQuake2

CMod_LoadBrushModel: maps/experiment1.bsp has wrong version number (3468 should be 38)

I know that the issue is texture related. the map has one texture, tried to change it. Does KMQ2 load the textures from pak0 or someplace else? Maybe i need older version of the Q2textures .wad?
Compiled it with tyrUtils.

can someone please HALP! 

Not texture-related. You used the wrong compilers, Tyrutils are not for Quake2. Q2map.exe is what you need, or some newer modified ones like these, for example: http://home.insightbb.com/~gryndehl/q2compile/quake2.html 

So guys I use trenchbroom for map editing and i was wondering how do i make a rectangular prism?? is there any guides on how to build more complex shapes in trench broom such as prisms? 

The Trenchbroom manual is literally (not hyperbole) the single best Quake related manual you will ever see. It will show you amazing things like vertex/edge manipulation etc. (what you need in this case) Just look for the help menu item. That will launch the manual. Kristian used to have a version online but I don't think it's up any longer.

Seriously take a 1/2 hour of your time and take a read. And FYI I have to refer to the manual quite often and forget or miss things... this it what manuals are for and the dev took the time to write it for YOU.