First, you are to be congratulated for your careful observation! One of the first rules of pest management is to be constantly looking out for harmful bugs. Second, identify what bugs you are dealing with. Most bugs (especially aphids) can be eliminated by simply spraying them off with a water jet. If your plants are small you can also try removing them from the media and letting them soak in the fish tank for at least 15 minutes. This drowns the bugs, and the fish get a treat. If neither of these techniques works we recommend an organic insecticidal soap/spray. Avoid any non-organic pest control treatment, as well as organic products containing Neem and Pyrethrum. Both are toxic to fish. And with any spray, no matter how safe, avoid spraying over the fish tank or rafts.
See the post titled “Aquaponics and the Battle of the Bugs: part 2″ in our blog for more detailed information.