Try to get your pond liner as high as possible, water pressure does a good job of pushing water out of seams. I had that issue with my arizona pond.
Use sealant, I would also get single side pond tape and tape the edges of the seam together. I used single side on the seams, double side between the two and sealant and still had seepage in arizona.
My stream in arizona also had rocks on it, all the way to the deep end, they did not keep the seepage from happening. We had to remove the rocks,
(if I remember right I cut the long piece of stream liner) pulled the stream liner back above the pond liner, started at the very top edge of the pond liner, goop, tape, on and on until the stream liner was around 2 feet down in the pond. Then single side tape on all of the edges..........finally no leak lol
My pond was 5 feet deep quickly learned water pressure would just push the water out. My sealant may not been applied thick enough, who knows, just know it leaked.
If you can get your shelves a little lower I would do it, herons will find your pond. Make it uncomfortable for them to stand and try to fish.