Generally speaking, we have the same basic layout. My stream is twice as long as yours, but if you attempted to hide and naturalize the stream well as I did, you likely have a overflow somewhere at the stream edge. If you kept the edges high as shown in your building pics, then perhaps that is less likely. That likely leaves a crack in your bucket, a split in your pump hose (unlikely), or a loose connection in the hose or at the bucket (quite likely). Of course, you could have damage to the stream liner which is a royal pain to find, but fortunately, unlikely unless you get lots of big critters in your system. Of course, the biggest critter stomping around your system may be you crushing the stream edge down. ; ]

Thank you so much for the response!! I ran a hose down through the barrel hose and checked "every" inch of the hose. No leak. No leak in the barrel or hose connection either. When I put down the stream liner I cut it so it overlapped into the bottom so I could pull it up and check for a leak if need be. I ran water down the stream and checked underneath, no leaks. I built a dam at each end as well just to be sure ( : No leaks underneath. Here's the kicker. I went over the pump. The hose between the pump and filter box didn't look to good...kind of squished.... plus the orings were wore out. Went to Lowes and got some stuff. Also tilted the barrel way down so it wouldn't take as much time to fill up. 3 hours later without adding water...everything is looking good. Crossing my fingers.

Well: I hope it is the o rings or the tipping barrel. However I don't see how it could be the o rings because if I see things right, the pump and filter box are sitting in the bottom pond and completely contained within the bottom liner. If the barrel were cracked near the top, a change in arrangement could stop things.
I don't understand how you determined the lack of leaks by running the garden hose thru the plumbing, but if things are OK, then its not important any more. One thing you mentioned is worth looking into except that things were OK for years. This is the overlap into the lower pond. I did something similar; and while I don't think it has caused me a problem, I can't be sure. If you haven't heard of capillary action, it is the placement of very thin tubes or filiments that draw liquid upwards. The over layment of liners can cause little gaps that act like tubing and draw water up and then crawl along and over the lower liner. When we overlaid our liners, we were supposed to place rough surfaced dividers between the liners to allow large enough air gaps to prevent the capillary action. Again, I doubt that this happened to you because things were originally OK, but who knows?
Of course, if you don't have a problem anymore, then Nevvverrrr Mind.