It seems the issue is not the physics, but the scale. Aquaponics is intensive. Natural, passive energy is not. Natural waterways circulate passively, but they use enormous scales to do it. How many gallons of lake water support each of the fish therein? Your passive warm/cool circulation could work in your totes--if you're looking to support a couple goldfish and a basil plant. It seems that for adequate circulation for anything more serious (that is, intensive) you need mechanical help, like a windmill.
For oxygenation particularly, you could circulate the water through several other totes that are chock full of water plants. In other words, you sacrifice some of your nutrient in order to produce oxygen. It's all a question of scale. You can't grow lots of fish on a little bit of oxygen. Even if you find something that can survive on lower oxygen levels, how healthy will they be really?