So what to do.. where to start... (
knew I wouldn't get this in before other posts... 
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So this implies that you need a starting baseline of your source water parameters...
A basic understanding of the baseline plant nutrient requirements through life span...
A basic understanding of what factors might alter base line water chemistry...
How your production method/design.. and environmental factors might alter your optimal parameters...
How you might control such factors...
What/how you can return to your optimal growth parameters...
And... What/how might prevent you from returning to your optimal growth parameters...
In aquaponics we are attempting to essentially grow two main groups of organisms...
There are others, mainly micro-organisms that are sometimes shared by both groups.. and are beneficial.. others that might be more specific to one than the other... and some that might be detremental to one, or the other or both groups...
Straight away the latter point concerning micro-organisms and processes suggests questions about potential areas of control, or lack of control...
Both productions groups share three common requirements... water, oxygen.. and nutrients....
So, in a commercial context... the very first requirement... is a baseline water analysis...
Oxygen and nutrient requirements are known for both fish and plants.... and the chemistries of fish and plant growth known as to how they will effect water parameters.. especially in a closed loop system...
Likewise the chemistries of most of the bacterial micro-organism process are known... and chemistries can be extrapolated...
But there other micro-organism processes... many of which can be deleterious to either fish, plants or both... that need to be understood and controlled...
With media bed systems... many of the biofloral micro-organisms are probably more akin to soil based systems.. within which they perform functions that might actually be beneficial, but in a recirculating system may be detrimental, even fatal to fish (particularly).. or even plants...
Controlling such processes requires that they be both identifiable, measurable and remediable.. in order to control them...
In media based AP systems... I don't believe that we can do any of the above.. with any level of quantatative certainty....
As such.. IMO.... media beds have NO place in a commercial aquaponics scenario.. that requires levels of control for consistent production...
Quite simply aquaponics is the combination of aquaculture and hydroponic (soil less) methods of plant production....
The only common denominator of combining the two production methods.. is the water and nutrients...
Separate the two production components.... literally and figuratively....and you can then apply controls accordingly...
And you can then test/measure and control adjust your parameters...
Build your fish system with known/proven RAS principles... the first of which is to remove the factors that are detrimental to fish growth and survival.... remove ammonia and solids from the fish system water.. totally... and treat them externally...
You can then also remove, or treat any detrimental micro-organisms and/or pathogens.. make any necessary chemical adjustments... and reuse the water...
Likewise.. adopt the very same approach to the hydroponic plant production system...
The only real common denominator... is the water... and it can be used for both components.. and reused...
Nutrient needs and supply to the fish system is relatively easy... just throw in the fish feed... (yes I know there's a few other things that need supplementation/adjustment)...
It's all been worked out for nearly every possible commercial, or potentially commercial species... and aquaculture can be a highly profitable enterprise...
Nutrient needs and supply to the plant system.. is a little more complicated... but again.. it's been worked out accordingly in the same vein... and hydroponics can be a highly profitable enterprise...
The biggest impediments to commercialisation of aquaponics are... IMO...
The romantic notion that somehow aquaponics is more than the sum of it's parts... and a self-defeating adherence to a belief of a "single closed loop"...
The adherence to backyard system designs that were/are essentially based on a "suck it and see" approach...
An inherent desire, or insistence... on re-inventing the wheel...
And the apparent lack of knowledge and/or understanding of either aquaculture, or hydroponic plant production... and issues of scale.... by those promoting current "commercial" aquaponic designs...
So CDM (and others).. if you're going to pursue a commercial integrated production system...
Identify and separate your component subsystems... and design them accordingly///
The baselines for both fish and hydroponic plant growth are known and understood....
The water is the commonality... test your water (regularly).. and adjust it accordingly.... to the parameters required for optimal growth... of either system...
All you have to do then... is sell the fish and/or plants... go forth and conquer....