Water Tunnels

Once the tunnel is cleared you start with the water.
Simply create three brushes that will fill the three
sections that make up the the tunnel.   Texture the
new brushes with a water shader from the liquids
section in textures.  Now when using liquid brushes
that border each other,  the textures will cause a
border effect.  The best way to stop this is with the 
'no draw' texture from the common section.  Make
sure  the  surface  you  choose to  change  on  the 
liquid brush is not on the top or bottom. 


   

I've taken the two side brushes and pulled them all the 
way down with a little space left at the openings in the
floor.   The  'no draw'  texture  will  be  on the side  of  the
brush that faces the center section.  The same has to
be done on either end of the center brush.  This way
all  touching areas  of the liquid brushes  will be  see 
through.  The last  step  is  to  add  some  light  in  your 
new tunnel.  Make sure that any illumination has an
actual  light  source.  Torches  would  probably  be  a 
bad idea, fire doesn't work too well under water.

   

Save the map, compile, and launch.