Unlike the usual setup, in which players run around in the volume space between all the brushes of your map, with water, players splash/swim about inside the brush.

To illustrate this, we'll flood one end of the little building we've made.

Block off one end of the room by making a low wall as shown.  It's caulked and been made Detail, and had some brick texture applied.

Then create a brush that is just a little bit lower than this new wall, but has edges that extend a little way into the floor and into the surrounding walls, rather than meeting them flush.  Use grid scale 4 to do this.  I have filtered models to make the view clearer.  See how the brush goes into its surrounding walls (and the ground, not visible in the overhead view).

Click textures/liquids/liquids_sd and select the siwa_waternodraw to texture the whole brush.  Then select just the surface face of the brush and apply siwa_water.  Then press ESC.

Only the surface needs to be visibly textured with water, the other faces won't be visible, but they can't just be caulk etc, they have to be a water-type shader; the siwa_waternodraw will do fine.

Save and compile the map, and go and splash around in it in ET.  If it were deeper you would be able to swim in it.