In aquaculture, the main drawback is having to "waste" 10% of water, cycling in fresh water while removing high nitrate water.

In hydroponics, the main problem is creating nutrient solutions.

In aquaponics, it is almost impossible to make a system that properly accomodates both fish and plants.(PH and water temp being the 2 bigest clashes)

My thoughts: Have 2 seperate, yet connected systems.

PART A: Aquaculture system, minus any biofiltration.

http://www.aps.uoguelph.ca/aquacentr...0(Jun2007).pdf
Check out the overflow setup on pg 6, Figure 1. If I were to stagger the height of each of those tanks by 6 inches, the overflow of first tank would flow into second. The wastes of each of those tanks would be able to settle into the clear portion of the overflow setup.

Benefit is that you would be able to run this system at a PH and temp optimum to the fish you are raising.

PART B:

At the bottom of the overflow assembly, install either a gate valve, or quarter turn valve to manually empty wastes into another pipe that connects to hydroponic system. These wastes would flow directly into a media bed(or possibly a bio chamber) filled with expanded clay balls, red worms, and high nutrient load plants such as tomato or watermellon.

Benefit is that you would have the waste being broken down in a system where the nutrients could be immediately put to use in the flowering of the plants in the bed. Additionally, since the waste is being broken down in a system outside the fist tanks, there really isnt much worry about having to change out fish water to remove the high level of nitrates in the water.