Zack, I'm 100% dizzy and nauseated, but at least I can see what you were trying to post last night. You want suggestions I'll give you my honest opinion. What you do is your choice. First off, get a water test and check your water. Not knowing what your water is doing is like not going to school and trying to be a Dr. Your never going to learn what your fish need or what condition they are living in if you don't. It is our responsibility to to care for the water, this is the life support system your providing for your fish. Would you want to be stuck in a 4 x 4 room full of chlorine and cigarette smoke. NOPE none of us do we want to breath clean air and that's what your doing by not testing the water, Speaking of which, stirring up that gravel like that and making it go down to your fish, No wonder he doesn't want to come out, It has a lung/Gill full of sand and silt, He's probably trying to gasp for some clean water to breath. Filter needs to be much larger, I run bigger filters on my 30 gallon tank and 75 gallon tank. That might work for a couple of 3" fish in a 40 -50 gallon pond. Seriously, for that size pond your filter needs to be three or fout times more surface are for the bacteria to grow on. Now for the stream. The gravel in the stream is fine, but using it for a filter, not so good, it's going to cover with algae and get gunk in it, Every time you stir it up where is it going? Right down into the bottom pond, going to build up and your going to have green water issues, If you go to larger rock where the water can flow through the rocks you won't get that effect as bad and the rock WILL grow bacteria on it because the water can flow through and give good surface area for the bacteria to grown on, as it is now you get very limited bacteria growth and your forming a anaerobic place for bacteria to grow causing more problems than good, each time you stir it up your releasing all that sand silt and anaerobic bacteria right down to your fish which eventually will cause health issues and possibly fungal and bacteria problems with your fish. I would take the middle pond/body of water and fill that with as many plants as possible and still get good flow back out into the main pond, This will be 3-4 times the filtering that the canister is doing, It will help lower nitrates, give more bacteria surface are for growth and will greatly reduce the fine particles in the water, By doing this also the debris that would be caught in the stream will get caught there so you can periodically remove the plants and suck all the build up off the bottom there and out of the system, GREATLY improving the overall conditions in the pond.