Aquaponics is not a cheap to start as like other forms of gardening or aquaculture. 

Expensive initial startup costs compared with soil vegetable production or hydroponics.

One should have good knowledge of fish, bacteria and plant production to be successful in aquaponics .

There is a problem that fish and plant requirements do not always match perfectly.

Aquaponics is  not recommended in places where cultured fish and plants cannot meet their optimal temperature ranges.

Reduced management choices compared with stand alone aquaculture or hydroponic systems.

Mistakes or accidents can cause catastrophic collapse of system..

Daily management is mandatory.

Monitoring of water is a crucial process in aquaponics so water testing should be done periodically.

Requires reliable access to electricity. In most cases electricity is needed to run a water pump and possibly aeration pumps as well.

Alone, aquaponics will not provide a complete diet.

Green house is needed for good aquaponics system which depend on the climatic condition of the place where aquaponics has to setup.

 One should have to keep in mind before starting aquaponics that If one or more components fail then this could lead to loss  of fish and or plants.

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