A successful aquaponics enterprise requires special training, skills, and management. (Rinehart, 2010)

Building and equipping a commercial-sized aquaponic greenhouse can cost $10,000 to $30,000, depending on the system design and choice of components. Due to the highly technical nature of aquaponics and the expense associated with greenhouse production, prospective growers are advised to thoroughly investigate production methods and market potential. (Rinehart, 2010)

Aquaponics has been discussed as a part of sustainable intensive agriculture, however there are several limitations to aquaponic food production that may make aquaponics a better or worse fit at certain scales or in some climates or regions of the world. The weaknesses of aquaponics, as described in a United Nations Food and Agriculture report, include: it is knowledge intensive, expensive to start-up, energy/resource demanding, requires daily maintenance, has fewer management choices than agriculture or aquaculture, requires access to fish and plant seed, the fish in the system have narrow temperature ranges, and mistakes or accidents can result in catastrophic collapse of the system. (Somerville et al, 2014)

Power outages in the winter can result in total loss of a tilapia crop, for example. Infestations of diseases or parasites can be difficult because only biological controls can be used in aquaponics units, as chemicals may kill the other crops integrated into the system. It is important to underestimate somewhat the growth and yield of fish and plants and to slightly overestimate the costs. The most challenging aspect of managing an aquaponics operation is to develop a realistic, accurate, and workable marketing plan. Raising fish indoors is two to three times more expensive than raising fish in open ponds. Thus, a profitable aquaponics operation will need to seek out and develop a market that will pay a higherthan-average price for the crop. An in-depth understanding of the level and type of competition in the market place is essential. For example, an individual who raises lettuce in aquaponics will need to compete with lettuce sold in Wal-Mart, in other grocery stores, and at farmers’ markets. Why would an individual buy aquaponically grown lettuce, especially if it is more expensive than other types? The seller must have a clear answer to that question to be competitive. Labor requirements must also be considered. An aquaponics system requires frequent attention. Even on a small scale, aquaponics systems are complex because of their multiple components and requirements. Disease prevention, water level control, and preventing rodents and other problems require inspection and care of the system throughout the day, 7 days a week. Harvesting and packing vegetables are also quite labor intensive. Tokunaga et al. (2015) estimated that labor costs were 46 percent of total operating costs and 40 percent of total annual costs. This is quite high compared to other forms of aquaculture and prospective aquaponics managers must be certain to have an adequate supply of labor to cover these needs. (Engle 2015)

A broad range of knowledge is required to understand and implement the multidisciplinary concept of aquaponics. From the theoretical perspective, the multidisciplinarity of the field and a lack of training in holistic thinking is a hurdle to fully comprehend the concept of aquaponics covering all interrelating issues. The bundling of field-specific in-depth knowledge is required in order to consolidate available scientific knowledge and evidence. At most universities, the two main disciplines, i.e., hydroponics and aquaculture, are either not taught, or offered in different schools, which could complicate access and exchange of knowledge. In practice, aquaculture and hydroponic technologies are well-known. The problem lies in the fact that those disciplines need to be connected. This lack of information-sharing shows the necessity for developing an education network dealing with the improvement of the interconnection between (scientific) disciplines involved in this field. Aquaponic stakeholders, including researchers, entrepreneurs and technicians, need to have basic knowledge covering all disciplines that are involved in this field. Furthermore, experts within every connected field are required to address specific issues within theoretical, scientific, financial as well as practical frameworks. (Goddek et al, 2015)

Savidov (2004) identified several sources of production risk in aquaponics systems, particularly in the first year of operation. Prospective growers should plan for a steep learning curve as they learn to manage the complexities of several crop systems that are linked to each other and that affect one another. Among the reported sources of loss in the first year of operation were high fish mortality, nutrient deficiencies during startup, selection of cultivars not well suited to aquaponics conditions, root rot, and flooding of the facility due to problems controlling water levels. Savidov (2004) also discussed food safety concerns expressed by consumers over aquaponics produce. In that consumer survey, respondents expressed concerns about bacterial counts in the water, whether there was adequate testing and monitoring of bacterial counts, and whether bacteria from the fish production unit would get into the vegetables. Aquaponics growers must be aware of these concerns and ensure that the vegetables and fish supplied are free of harmful substances. (Engle 2015)