Water sometimes cuts horizontally though the map when its compiled but its supposed to fill the brush volume with water. I dont think there is a perfect solution but i would try one of these.
Make sure it has structural brushes around it to define the boundaries.
Try using a no_draw_decal brush with water texture on one face.
If none of those suggestions work i have a dynamic water texture and a scrolling foamy texture/model i used for a waterfall and stream i might be able to upload.