If it were mine, I would put liner up and under the spillway and up the wall edges. Secure it well to the box. I would then get a good silicone, roofing goop or use Goop for marine use, more expensive but that stuff is made to be under fresh and or sea water.
Apply a good layer to the spillway and a layer to the box, let it get a bit tacky then attach. Don't touch for a few days. The goop hardens like a rock. The roofing goop stays a bit flexible, silicone has failed a few times for me, releasing.
Also stick the two rock edges to the bottom rock. I don't recall is the box sitting on the edge of your pond, ie where the spillway edge is, is it hanging over the pond? If it is any little leaks will drip into the pond.