Use the block tool to make a block of what will be your water.

Place the block of water were you want and make sure it stays as a block, you cannot make it slanted, etc.

Use the texture tool and apply the nodraw texture to all sides but the top of your water block.

For the top texture choose a water texture of your choice and apply it to the top only.. The rest should still be the nodraw texture.

Now you need an entity called the water_lod. Just place it by the water or on top is fine. No changes are required for the entity as it just controls the way the water changes quality...

Next, place another entity called env_cubemap on top or by the water.

Open up the entity's properties and go to the second option and click the pick button and select the top of the water.

Now when you compile your map you should have working water ^^

If you need help on this just post here I'll help yeh :D