The pond looks very well made. Looks like maybe a concrete collar around the pond rim under the liner.
I don't know how warm it's been in Kansas lately, or more importantly the humidity and wind, but at least some of that 2" loss is evaporation. To get a reading on evaporation you can set out a straight sided container, filled with pond water, in the stream to keep temps the same. The loss won't match the pond because you have the stream and everything above the pond. And all the evaporation shows up in the lower pond. I once had a bunch of interconnected ponds and the amount of loss in the lower pond could be scary.
I'll say this, it's not unusual for a person new to pond to be surprised by the amount of water loss by evaporation. 2" is a lot, but possible if that was just a guess and it's really closer to 1". I'm just not sure how close a measurement this was.
After I was sure it wasn't evaporation I start looking for leaks.
A leak in one spot that draws down that size pond by even an inch should create a real swamp assuming clay soil. Standing water type deal. So there should be a lot of easy spots to check by just stepping along the edges.
Assuming all the easy to check places have been checked the next place I go is to where the water enters the pond. I'd probably move some rocks. Stick your hand into any dirt looking for serious mud. Many a waterfall I've built have leaked. Just the nature of the game when you want a natural looking waterfall. They have to be tweaked sometimes.
As was already said, turning off the stream for a few days is easy way to localize the issue. But be careful here. The pond will lose less water from evaporation without the stream even if there isn't a leak. Streams create a lot of surface area for evaporation. So if the pond goes down 1" instead of 2" I would not automatically assume there is a leak in the stream.
If there's a leak in the stream you can bypass sections using sand bags (panty hose work great along with plastic) to build dams and a pipe to divert. The dams don't have to be 100% water tight, but as best you can. First dam half way up the stream, then you know upper or lower. Halve that section again. 3 or 4 tries will get you within a few feet of a leak.
Another possibility is there isn't a single leak, but instead lots of little things. Does the wind blow water off the water falls and out of the pond? The rocks in the beautiful stream could be wicking water up and over the liner and out. Plant roots could be growing over the liner under the rocks and into the water.
I generally end up taking up almost all the rocks looking for a leak.
One thing I wouldn't do is start guessing. Gooping up stuff hoping that was the leak. It can make things worse and is a waste of time. When the leak is found it's generally easy to fix by just moving a few rocks. Even a hole in the liner in the stream can be fixed by putting a rock under the liner to get the hole above water and you're done.
The silver lining is this is a really good way to get to know your pond. Good hunting.