Shrimp farms worldwide have been responsible for a series of social and environmental issues that affect their surrounding regions. Modern aquaculture seeks to achieve sustainable growth that offers a balance between environmental, economic, and social perspectives, and new aquaculture technologies have been developed and improved in recent decades. One such innovation is the biofloc technology (BFT) system, which is considered an alternative to conventional aquaculture because it allows for aquatic organism production with minimal water exchange, high stocking densities, and the possibility of high levels of productivity. Life Cycle Assessment (LCA) is one of the most common methodologies used to compare the environmental performance of different systems, considering resource consumption and the emission of pollutants during the productive life cycle. The present study uses LCA to compare the environmental performance of Penaeus vannamei shrimp production in two BFT systems, an intensive system in a pond and a super-intensive system in a greenhouse. The Functional Unit used was 1.0 ton of shrimp (animals with an average final weight of 12 g). The boundaries of the system were defined as from the cradle to the farm gate. Input data related to the use of natural resources, energy consumption, and environmental emissions were obtained over eight cycles of intensive and super-intensive production. The following results were obtained for intensive and super-intensive systems, respectively: global warming (GWP100a) 5691.12 and 5512.42 kg CO2 eq; acidification 59.57 and 59.05 kg SO2-eq; eutrophication 25.96 and 25.80 kg PO4 eq; ozone layer depletion (OLP) 0.000319 and 0.000311 kg CFC-11 eq; human toxicity 1165.98 and 1233.33 kg 1.4-DB-eq; aquatic ecotoxicity 1344.13 and 1925.96 kg 1.4-DB eq; marine ecotoxicity 1881,643.65 and 2070,517.23 kg 1.4-DB eq; terrestrial ecotoxicity 24.26 and 33.54 kg 1.4-DB eq; photochemical oxidation 2.10 and 2.03 kg C2H4 eq; abiotic depletion 0.006487 and 0.008359 kg Sb eq; abiotic depletion of fossil fuels 35,612.80 and 34,504.39 MJ. Among the eleven evaluated impact categories, the intensive system showed better results in five categories, while the super-intensive system showed better performance in six categories. Feed (reference diet) was the most significant factor in the environmental performance of the evaluated systems. Based on these results, we conclude that feed and electricity had the most environmental impact in both systems. In general, when comparing the use of production factors and productivity between the systems, it becomes more evident that the SS is more efficient than the SI.