My water acts the same way as a skybox ingame.
Above is in hammer. Below is in game. Halp, please. 
Most likely a leak.
Just put brushes around the water and it will be okay.
Just to make sure though, press map>load pointfile and see where the red line goes to, if it asks you to select which one you want to use then you don’t have a leak. If that happens post the compile log.
No leak.
Edit: Silly me. Leaks galore.
Compile log:
** Executing...
** Command: "c:\program files (x86)\steam\steamapps\zeebie\sourcesdk\bin\orangebox\bin\vbsp.exe"
** Parameters: -game "c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2" "C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7"
Valve Software - vbsp.exe (May 19 2009)
2 threads
materialPath: c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2\materials
Loading C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7.vmf
Brush 58529, Side 6: duplicate plane
Brush 58529, Side 10: duplicate plane
Brush 58529, Side 14: duplicate plane
Brush 58529, Side 18: duplicate plane
Brush 58529, Side 22: duplicate plane
Brush 58529, Side 26: duplicate plane
Brush 58529, Side 30: duplicate plane
Brush 58529, Side 33: duplicate plane
Patching WVT material: maps/gm_explore_a7/concrete/blendconcreterock001a_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blendgrassdirt03_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blendashdirt01_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blendrockblack02a_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blenddirtmud01_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blendrockblack02a_dx8_wvt_patch
Patching WVT material: maps/gm_explore_a7/nature/blendrubbledirt001a_wvt_patch
fixing up env_cubemap materials on brush sides...
ProcessBlock_Thread: 0...1...2...3...4...5...6...7...8...9...10 (0)
**** leaked ****
Entity light_environment (137.21 -1234.69 5080.00) leaked!
Processing areas...done (0)
Building Faces...done (0)
Chop Details...done (0)
Find Visible Detail Sides...
Merged 4 detail faces...done (0)
Merging details...done (0)
FixTjuncs...
PruneNodes...
WriteBSP...
done (0)
Creating default LDR cubemaps for env_cubemap using skybox materials:
skybox/sky_day01_09*.vmt
! Run buildcubemaps in the engine to get the correct cube maps.
Creating default HDR cubemaps for env_cubemap using skybox materials:
skybox/sky_day01_09*.vmt
! Run buildcubemaps in the engine to get the correct cube maps.
Finding displacement neighbors...
Finding lightmap sample positions...
Displacement Alpha : 0...1...2...3...4...5...6...7...8...9...10
Building Physics collision data...
done (1) (243265 bytes)
Placing detail props : 0...1...2...3...4...5...6...7...8...9...10
Water found with no water_lod_control entity, creating a default one.
Compacting texture/material tables...
Reduced 2409 texinfos to 1095
Reduced 80 texdatas to 69 (2202 bytes to 1822)
Writing C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7.bsp
7 seconds elapsed
** Executing...
** Command: "c:\program files (x86)\steam\steamapps\zeebie\sourcesdk\bin\orangebox\bin\vvis.exe"
** Parameters: -game "c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2" "C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7"
Valve Software - vvis.exe (May 19 2009)
2 threads
reading c:\users\zeebie\documents\mapping+modeling\Gm_Explore_a7.bsp
reading c:\users\zeebie\documents\mapping+modeling\Gm_Explore_a7.prt
LoadPortals: couldn't read c:\users\zeebie\documents\mapping+modeling\Gm_Explore_a7.prt
** Executing...
** Command: "c:\program files (x86)\steam\steamapps\zeebie\sourcesdk\bin\orangebox\bin\vrad.exe"
** Parameters: -game "c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2" "C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7"
Valve Software - vrad.exe SSE (May 19 2009)
Valve Radiosity Simulator
2 threads
[Reading texlights from 'lights.rad']
[48 texlights parsed from 'lights.rad']
Loading c:\users\zeebie\documents\mapping+modeling\Gm_Explore_a7.bsp
No vis information, direct lighting only.
Setting up ray-trace acceleration structure... Done (0.60 seconds)
3224 faces
871190 square feet [125451472.00 square inches]
3 Displacements
12015 Square Feet [1730212.13 Square Inches]
293 direct lights
BuildFacelights: 0...1...2...3...4...5...6...7...8...9...10 (55)
Build Patch/Sample Hash Table(s).....Done<0.0219 sec>
FinalLightFace: 0...1...2...3...4...5...6...7...8...9...10 (3)
FinalLightFace Done
18 of 20 (90% of) surface lights went in leaf ambient cubes.
ThreadComputeLeafAmbient: 0...1...2...3...4...5...6...7...8...9...10 (24)
Writing leaf ambient...done
Ready to Finish
Object names Objects/Maxobjs Memory / Maxmem Fullness
------------ --------------- --------------- --------
models 58/1024 2784/49152 ( 5.7%)
brushes 556/8192 6672/98304 ( 6.8%)
brushsides 4295/65536 34360/524288 ( 6.6%)
planes 5002/65536 100040/1310720 ( 7.6%)
vertexes 6721/65536 80652/786432 (10.3%)
nodes 3287/65536 105184/2097152 ( 5.0%)
texinfos 1095/12288 78840/884736 ( 8.9%)
texdata 69/2048 2208/65536 ( 3.4%)
dispinfos 3/0 528/0 ( 0.0%)
disp_verts 451/0 9020/0 ( 0.0%)
disp_tris 768/0 1536/0 ( 0.0%)
disp_lmsamples 30830/0 30830/0 ( 0.0%)
faces 3224/65536 180544/3670016 ( 4.9%)
hdr faces 0/65536 0/3670016 ( 0.0%)
origfaces 1913/65536 107128/3670016 ( 2.9%)
leaves 3346/65536 107072/2097152 ( 5.1%)
leaffaces 3745/65536 7490/131072 ( 5.7%)
leafbrushes 1329/65536 2658/131072 ( 2.0%)
areas 3/256 24/2048 ( 1.2%)
surfedges 23676/512000 94704/2048000 ( 4.6%)
edges 13802/256000 55208/1024000 ( 5.4%)
LDR worldlights 292/8192 25696/720896 ( 3.6%)
HDR worldlights 0/8192 0/720896 ( 0.0%)
leafwaterdata 1/32768 12/393216 ( 0.0%)
waterstrips 294/32768 2940/327680 ( 0.9%)
waterverts 0/65536 0/786432 ( 0.0%)
waterindices 4779/65536 9558/131072 ( 7.3%)
cubemapsamples 0/1024 0/16384 ( 0.0%)
overlays 0/512 0/180224 ( 0.0%)
LDR lightdata [variable] 3344064/0 ( 0.0%)
HDR lightdata [variable] 0/0 ( 0.0%)
visdata [variable] 0/16777216 ( 0.0%)
entdata [variable] 89906/393216 (22.9%)
LDR ambient table 3346/65536 13384/262144 ( 5.1%)
HDR ambient table 3346/65536 13384/262144 ( 5.1%)
LDR leaf ambient 12965/65536 363020/1835008 (19.8%)
HDR leaf ambient 3346/65536 93688/1835008 ( 5.1%)
occluders 0/0 0/0 ( 0.0%)
occluder polygons 0/0 0/0 ( 0.0%)
occluder vert ind 0/0 0/0 ( 0.0%)
detail props [variable] 1/12 ( 8.3%)
static props [variable] 1/976 ( 0.1%)
pakfile [variable] 215052/0 ( 0.0%)
physics [variable] 243265/4194304 ( 5.8%)
physics terrain [variable] 1202/1048576 ( 0.1%)
Level flags = 0
Total triangle count: 8915
Writing c:\users\zeebie\documents\mapping+modeling\Gm_Explore_a7.bsp
1 minute, 23 seconds elapsed
** Executing...
** Command: Copy File
** Parameters: "C:\Users\Zeebie\Documents\Mapping+Modeling\Gm_Explore_a7.bsp" "c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2\maps\Gm_Explore_a7.bsp"
** Executing...
** Command: c:\program files (x86)\steam\steam.exe
** Parameters: -applaunch 420 -game "c:\program files (x86)\steam\steamapps\zeebie\half-life 2 episode two\ep2" +map "Gm_Explore_a7"
There’s your leak…
Oh noooooo. Okay, I’ll just surround it with a super special skybox like I was going to anyway.
[editline]10:39PM[/editline]
Nope. It’s still happening.
Never do this. Surrounding entire map with a box is dumb.
Oh really? :0 Whoooops.
Wow…
Hey, Mister omniscient, I’m a relatively new mapper, and this seemed like a legitimate and fast tactic to me. I appreciate your help, though. 
Yes, supreme overlord.
Brush 58529, Side 6: duplicate plane
Brush 58529, Side 10: duplicate plane
Brush 58529, Side 14: duplicate plane
Brush 58529, Side 18: duplicate plane
Brush 58529, Side 22: duplicate plane
Brush 58529, Side 26: duplicate plane
Brush 58529, Side 30: duplicate plane
Brush 58529, Side 33: duplicate plane
You also have a bunch of duplicate planes. If I remember correctly, it means that a brush has a “corner” on a straight line so it’s not really a corner at all. There should be an option to “Go to brush number” somewhere in the toolbar thingy in the top-part of the screen. It should also pop up by pressing ctrl + shift + G. Type in the Brush numbers specified above and fix them.
Fixed that. It was a cylinder that was fucked up.
Also if you did not already, add a water_lod_control.
I will. Is that important?
An entity used to control the LOD behavior of any water in the map. If your map has water, this entity is required.
The properties of this entity apply to the whole map. Multiple instances of this entity within a map may cause errors.
Thanks! I did not know that. Let’s hope that worked. Checking now.
These sites are your best friend 
http://www.interlopers.net/tutorials/
http://developer.valvesoftware.com/wiki/Sky_List
The water LOD thing didn’t work. Checking out the site.
Fix the leak, load point file and find where the red line leaves.