it can be simply identified as removing of chemical and organic compounds which are harmful to aquatic plants or animals. Such as ammonia, nitrate, H2S, CH4, and improving dissolved oxygen level, correction of acidity or alkalinity of water as required.
The answer you seek also depends on the kind of system you are talking about.
The bio-chemical processes that can and do take place will differ greatly between a natural, self-sustaining lake used by local fishermen for subsistence and a pond used for large-scale, high density, high input prawn aquaculture.
Is there any particular type of system that you are referring to?
There is a vast amount of literature available on water filtration, and I have attached some references for you.
In simple words, there are three different parts to water purification or filtration. The first is suspended solids, the second is dissolved solids and lastly are the bio-chemical or metabolic waste products.
Suspended solids (SS) are waste products produced, but also includes uneaten food, algae and other flocculated material.
Dissolved solids (DS) can consist of salts, mineral compounds, micro-nutrients, leachates and various other micro-particles.
In the case of prawn farming which uses flow through systems, the amount of SS and DS in the water will depend on the flow rate and rate of water exchange in the ponds. Often some of these will remain in the ponds and contribute to the natural productivity of the pond.
However, if overfeeding occurs or water exchange is too low, then we can expect eutrophication to occur and then a crash in the any food web or mesocosm that has established in the pond, due to low oxygen and build up of harmful metabolic wastes.
This brings me to bio-chemical or metabolic waste products. If allowed to accumulate, these can cause mortality to the stock and also overwhelm the nitrifying and denitrifying bacteria populations in the sediment, as well as stripping oxygen from the water body due to increased biological oxygen demand.
The removal of bio-chemical or metabolic compounds in prawn farming, where flow through systems are used, can only be done by reducing feeding and increasing water exchange in order to reduce the concentration of these harmful products.
These are some excellent references that cover the subject of water quality management in aquaculture:
1) Pond Aquaculture Water Quality Management (Book)
By Claude E. Boyd
2) Aquaculture and the environment (Book)
T.V.R. Pillay
I have seen a few articles on Google Scholar, but to find what you need, it is best to read these books or something similar and then search for more specific information. If there is any further detail you need, I am happy to help you find more information.
A new approach of coupling aquaculture with green house has clear advantages - cleaning of aquaculture wastewater by delivering nutrients for growing vegetables.
Yes, so called aquaponics, although I am skeptical of it, because the protein rich diets for the fish usually translate to high Nitrogenous wastes, but there are a lot of plants used for human consumption which cannot take advantage of such phosporus deficient effluents that come out of aquaculture production systems. That is what I understand to be the major limitation of aquaponics, and in particular, it is supposedly one of the main reason why it is not yet a commercially viable practise. Regarding the suitability of aquaponics as a water filtration mechanism, I believe that for those reasons and the large plant surface areas required, it is not very efficient.
of course both fish production and vegetable production should be in equilibrium. And I do not mean mass culture. Further, fish and vegetables have to be selected carefully to assure synergism. Protein rich diet is not a must. Carp like fish e.g. can be feed on maize or similar. Adjustment of nutrient balance is also an option if entire balance is not achieved.