A bit of an "out there" suggestion: for the water surface, use thin (2-3 mm?) plexiglas or acrylic. Paint it with the appropriate muddy blue-green water color on the underside and use clear Modge Podge or other acrylic medium to make subtle waves on the topside. Attach low brick walls to the edges of the acrylic, with terrain modelling to fair the surface down onto your table top.
No warping problems. Pricier than MDF or the like, but dead stable. A little self-adhesive felt on the undersides will keep the canal segments from sliding around on your table...