The second difference comes from the varying components. hydroponics systems are very sterile, and there is no need for any extraneous growing media to support the plants or root systems. aquaponics, on the other hand, needs an environment around the roots to harbor the beneficial microorganisms.. Hydroponics vs aquaponics doesn’t have to be an either/or proposition. hydroponics and aquaponics follow many of the same principles, even though the methods of nutrient delivery differ. while fish tanks are a necessity for aquaculture, system designs are similar for both..