You just have to extract all the files from the game and edit the values.
The files are in tf/tf2_misc_dir.vpk so you will need GCFScape to open it. Once you have that opened, navigate to materials/water and find the water files that are closest to what you want to create. In my case it's water_well, water_well_beneath, water_well_dx80 and water_well_beneath_dx80. Copy these to tf/materials/water and rename them. In my case I replaced "well" with "powerup". Open the files in notepad and make sure to edit the name sof the other files that are being mentioned. Now change values like "$fogcolor" to whatever color you want. The color format is a simple RGB going from 0 to 255.
If you can't get it to work, ask somebody for help. Water materials can get a little confusing to work with.