@iSpectra: as I told you and also Felix said, you must look into the file
pak01_dir.vpk. This is a packed special file that Valve games use: many of the games' files are packed into there, not in common folders outside
Above I told you where it is located and how to open it. I suggest you to check into it and start by modifying any of the stock water materials.
There aren't tutorials for creating custom water materials, only for applying it properly... Be sure you also read the article Adding Water.
The VDC explains what each parameter does, but let me help with what I know:
water parameters
||Water //this is the shader type; it's one of the most complex ones! but because of that you can achieve awesome results. Normally, world textures use the shader 'Lightmappedgeneric', models use 'Vertexgeneric', and there are many more such as 'refract', 'solid energy'....
{
$forceexpensive 1 //this is telling the engine to render expensive water (high quality water with great reflections and such) instead of cheap; this can be also controlled by the water_lod_control that you must place on top of the water material in the hammer editor
$normalmap "liquids/water_river_normal_sharp" ** //this is similar to the bumpmaps for the world textures, the normal maps modify the 'height' of pixels and when you see the texture there are parts that appear to be embossed like; this is how the water_river_normal_sharp looks like:
$flowmap "liquids/sp_a1_intro5_hflowmap" //the flowmap is the map that tells the angine the directions we want the water to be moving; the different colours mean east-south-north-west.... This is how it looks like:
About the following parameters just read the VDC and if you want, play with their values to see the effect:
$flow_normaluvscale 160 //read the VDC
$flow_worlduvscale 0.5 //read the VDC
$flow_timeintervalinseconds 0.6 //read the VDC
$flow_uvscrolldistance 0.1 //read the VDC
$flow_bumpstrength 1 //read the VDC
$flow_noise_texture "liquids/water_noise" //this is a cool parameter, it introduces noise in the image of the water you see; check how it looks like:
$flow_noise_scale 0.001 //read the VDC
$flow_debug 0 //read the VDC
$basetexture "liquids/toxicslime_color" //THIS ONE is what you were looking for; this is that ugly goo look the water has in Portal2; even though not mandatory to make a custom water texture, Portal series use it to make the water looks toxic and ugly 
. This is how it looks like:
Let's do this: I've made a quick clean water material for you, download it from here and place it somewhere into your materials folder; then edit this line to make it point to the path where your texture is placed; for example if you put it into portal2/portal2/materials/liquids folder, this line will be like so:
$basetexture "liquids/jose_clean_water_test"
About the following parameters just play with them if you want, or leave them as they are...
$color_flow_uvscale 300
$color_flow_timeintervalinseconds 5
$color_flow_uvscrolldistance 0.11
$color_flow_lerpexp 1
$color_flow_displacebynormalstrength 0.01
$reflecttexture _rt_WaterReflection //Taken from the VDC: Texture to use for reflection. For real-time reflections, use _rt_WaterReflection.
$reflectamount "0.1" //This is the amount of warp for the reflection. Higher values produce more visible reflections
**$reflecttint "{ 240 240 192 }" ** //this is very interesting: it defines what color will have the reflections you'll see on the water's surface; that value is "white-ish", clear reflections, I like it (but you can also make reflections look more red or green if you like...); for the RGB colours in mapping, bookmark this site
**$reflectentities 0 ** //if set to "0" it won't reflect entities; I like to set it to "1" to see cool reflections of surrounding entities 
$reflectonlymarkedentities 1 //this is to reflect those entities with the property "Render in Fast Reflections" set to YES.
**$reflect2dskybox 0 ** //this is used when there's a skybox around; you set a value of "1" if you want your sky to be reflected on the water's surface, or "0" if you don't want it to be reflected.
(About all this, I made a post some time ago that I recommend you to read in the case you are interested in going a bit further regarding water reflections and skybox. Find it here )
$abovewater 1 //very important: this is satying that this whole material file is intended to be used for the above surface of the water brush, it's the "water itself"
**$bottommaterial "nature/toxicslime002a_beneath" ** //it's a required parameter; water needs an anove material (this one) plus a botttom material. This one is the typical you see when you submerge into the goo (brownish and dirt).
**$fogenable 1 ** //this is to enable the fog; it creates a fog you can see in the water; the following are the paramters that you can change to tweak it:
$fogcolor "{ 58 35 20 }" //this is oneof the most coolest parameter... it is the color you see in the water depth... the VDC recommends you to use a color that fits to the bottom material, up to you (I use a dark blue one though)
**$fogstart 0 ** //the distance in inches from the player's eye where the fog starts... it's recommended to use a value of "0" for edge fading to work properly
**$fogend 100 ** //distance in inches where the fog ends; to my experience this gives a sense of depth when you look into the water closely and zoom in...
**$lightmapwaterfog 1 ** //allows the fog to receive lightmaps, that's to say, it casts shadows coming from static props.
**
$flashlighttint 1** //to be frank I haven't really tested this parameter...
"%compilewater" 1 //needed to compile the water properly.
**"%tooltexture" "nature/water_frame01_normal" ** //this is just the image you see in your hammer editor texture browser.
$surfaceprop slime //use 'slime' or 'water', no significative difference; like the rest of the game textures this tells the engine what material is its surface made of, in order to adjust its behavior 'in game': a wooden material makes a particular sound when you walk on it.... a metal material too... glass or grates are handled/rendered in a special way... ||
Try that material I linked you to and let me know if it works good... As I told you the .vtf you posted has no alpha channel, and the water shader makes use of it to alternate the texture with the noise and flowmap... and to make it looks good with a cool movement.
Ok, now I'm a bit tired of writting, bye 
