The best aquaponics fish food falls into two categories: diy fish feed; commercial pellet feed; in this article, we will discuss the different feed based on fish diets, plus the best food you can give to your aquaponics fish. feeding fish in an aquaponics system. different fish species require different diets. some fish are herbivores, while others are strictly carnivores.. Very similar to trout, salmon is an excellent fish for aquaponics. not only is it a great producer of nutrients due to its size and diet but it’s also equally as durable as trout while offering a delicious taste and unique red coloring that people absolutely love..