Early on, I had a lot of trouble getting the flood and drain system to work correctly. Substrate would get caught in the siphon, and prevent it from initiating the drain.
Once the flood and drain system was working, I ran into issues related to my use of heterogeneous substrate. I had both hydroton pellets and perlite in the grow bed. When you mix substrates of multiple densities, both of which are lighter than water, the flood and drain cycle will result in the lightest substrate filtering to the top of the bed. This caused all of my plants to sink into the water.
After solving that problem, it became a simple matter of fish nutrition. I live in Colorado, which has very hot summers. Around 90°F is typical, but in the evenings the temperature gets down quite low. As it would happen, the average daily temperature was between 60 and 70°F. Fish modulate their diet according to the temperature of the water that they're in. And my koi would not eat enough.
In the end, the project was a lot of fun and I learned a lot. But I couldn't justify repeating the effort after all of the fish died in the winter. It didn't seem humane.
