Aquaculture, like any other biological production system, depends on external and internal sources of energy that may be regarded as renewable and non-renewable. Since an appropriate evaluation of energy flows through ecosystems sheds light on their dynamics and sustainability, the economic evaluation of the aquaculture system under study was paralleled by the application of the emergy method. The latter is an innovative and holistic environmental approach accounting for the direct and indirect solar equivalent energy (hereafter termed “emergy”) supporting ecosystems complexity and production of resources. The fraction of renewable emergy used up in relation to the total emergy supporting the process can be considered as a reliable and comprehensive index of a system′s renewability on the larger scale of the biosphere. Such a quantitative evaluation of sustainability is capable to support environmentally concerned decision-making according to the Agenda 21 Agreements. The emergy-based synthesis and the economic analysis combined together could provide valuable scientific information to support public policies for joint economic development and environmental protection. In the investigated case of the aquaculture system, incentives and policy measures for appropriate water consumption and decrease of water pollution can be related to emergy accounting results and indicators, in order to allow a transition to more sustainable aquaculture systems. This paper studied a typical fish farm with 3.4 ha occupied by ponds in Beizhuang District, located in the up-reach of Miyun reservoir. Energy systems diagrams as well as datasheets with matter and energy inflows were designed in order to calculate emergy indicators of the fish farming performance and sustainability. The emergy indices obtained are as follows: Transformity of produced fish is 1.33×106 seJ/J, Renewability is 15.53%, emergy yield ratio is 1.18, emergy investment ratio is 5.43, environmental loading ratio is 5.44, emergy exchange ratio is 4.63, emergy index of sustainability is 0.22. Although these indices revealed some similarity with China conventional agricultural systems, a careful evaluation of data and performance indicators shows that a fish farming system is less dependent on non-renewable resources and its renewability factor is greater than other animal production systems. The results of economic analysis finally indicate that a good environmental performance may also provide acceptable and sustainable economic results.