Scott,
Now that I have up to about 500 lbs. of trout in the pond I run the well pump 24/7 up until harvest to avoid any possible ammonia issues. However last fall I shut the well down when the fish load was half of what it is now and never did detect any ammonia or nitrite readings even with continuous feeding.
My last group of fish I had some morts and fish with problems after I shut down the well in the fall and came to the conclusion that it was water quality related or parasites increasing. I didn't have any experience testing for ammonia and nitrites at the time. Something I picked up after setting up the RAS tanks.
If the trout are just planted at 6 to 8 inches I crank up the well later in the spring and shut it down earlier in the fall to conserve electrical costs.
There is a possibility if I shut the well down and the water clears in the fall (due to the iron settling) there is a higher likelihood of males fighting, which I don't want. They are more likely to be more terretorial if they can see each other better.
I had issues like this with some of the last group of brook trout after I shut the well down. Looks like some kind of protozoan parasite irritating the skin to me. A salt dip seemed to have made the fish much better. One trout farmer I showed the picture to thought it might be from fighting. And it was to much a PITA to get a live fish to Purdue.
