Black roots?

I am getting a form of root rot on my plants. I have sense been turning the water off and allowing everything to dry out. I have the plants growing in a perlite and sand type mix and the pump flows a think moving stream of water under the plants. I have been unable to figure out what is causing this root rot. Some of these plants are natural aquatics and this does not seem to be making much sense. I have not added any fertilizer to the water for many weeks. Any idea how to prevent this in the future?

H202