First of all, I think you have a lot of great resources to make a nice waterfall, and I'm sure you can do something nice.
I am having trouble visualizing what you are talking about and all of the details and variables involved. I think you would get further with advice and your own personal clarity if you simplified everything into a diagram. Even on a piece of paper.
I'll throw out some general comments and hope it helps.
It seems to me that you are trying to implement a CHOP (
Constant Height One Pump) system. That makes sense for simplicity, and given the slope you have to deal with. In this scenario, think of the grow bed as your waterfall. (as it happens, I think your waterfall should *be* a growbed but we'll get to that.)
Constant Height One Pump is not always accurate. I recommend having two pumps for redundancy, following the same path. Or slightly different paths if you want a cool "merge" effect. You don't have to start out that way but its nice to have for peace of mind: the pump is the one thing likely to fail.
Check out the head height on your pump to see if it can handle the elevation/slope you have, and if so, what the decay in GPH will be. There is usually a chart.
A milk crate on the bottom to hold the pump does not seem adequate to me. It seems unstable and also not tall
enough. Given the shape of that depression and the greenery around it, I wouldn't be surprised if you get 2 feet of leaves and debris in there. The pump will clog. If it does it may overheat and fail, or at the very least not pump water.
I hope you have access to a power main. High GPH pumps are terrible
solar citizens in my experience.
Water seeks its own level. If you have clay soil up the slope, you shouldn't technically *need* the pond liner for the falls. It will flow down the lowest channel. However, like you, I would try to line the water paths just to have some control, and prevent erosion.
Goldfish are good because they can tolerate low temp and are omnivorous. They are very dirty fish and excrete a lot of ammonia. That's great if you have a lot of filter media surface area and plants to drink up the effluent. If not, the pond will pollute and there will be a nitrate spike, choking out the available oxygen and iirc correctly upsetting pH balance.
Which leads me to the growbeds. If you are already pumping fish waste uphill to trickle down, no need for a dedicated filter. Make little pools on the way down, fill with scoria/lava rock/pea gravel/cocofiber/etc, and they will build up beneficial bacteria. Bonus is they are a perfect medium for lettuce, spinach, broccoli, tomatoes, squash, etc etc. Or simply plant with aquatic ornamental plants.
Also have some of those plants in the water in case the pump fails. Fish food and insurance.
As for sealing the pond? Gleying is certainly an option, as is compaction. You could put bentonite plugs into the sidewalls but I'm not sure how much that would help. A true gleying with anaerobic organic matter is going to take some time.
Good luck!