Aquaponics is an emerging industry promoted as a sustainable agricultural practice. Economic sustainability of aquaponics is challenging, partly because some of the benefits are external to the grower, necessitating public intervention to support the industry. We used life cycle assessment to estimate the environmental impact of a proposed aquaponic system and applied a set of economic valuation methods to assess the costs of identified impact factors. We found that the system, planned to produce 60,000 ornamental fish and 108,000 lettuce heads per year would impact the environment with a cost of 10,700 EUR annually, about half the environmental cost of separate production of the same produce. Most of the external cost can be attributed to the industrial processes that prepare products used for aquaponic production. Although this method provides only a rough estimate of actual system impact, it can potentially be used to assess the cost-effectiveness of aquaponics from an environmental perspective.