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I know this may sound stupid...

But aside from sitting there and watching (because he still runs away from me ), how can I tell if my little RES is eating his pellet and not just letting it disintegrate into the water? I haven't seen any leftovers floating around but I also haven't seen him munch down?

You can leave some at the edge of his basking area to see if he is grabbing them.

Pellets take a long time to disintegrate into the water, a days time at least so if your seeing pellets gone within a couple hours his probably eating them.

I'm feeding my two hatchlings in a separate container right now. The bigger one eats faster and I wanted to make sure the little one was getting his share so they each have a container. You may want to try that for a couple of days just to make sure he's eating.

If you don't see any pellets, he probably ate them. It depends on the type of pellets, but they usually remain whole in the water for a couple of days. So you would definitely notice if he is not eating.

The idea about feeding in a different container is also good, especially when you have more than one turtle. It lets you control how much each turtle is eating and it also eliminates competition between them.