Concern about environmental impacts of aquaculture and its interaction with natural resources is increasing. Thus, it is important for new production systems to use practices that reduce environmental impacts, such as choosing to farm native species from a region's biological diversity and adopting better effluent management. This study aimed to estimate and compare environmental impacts of tropical freshwater prawn farming systems based either on the introduced species Macrobrachium rosenbergii (giant river prawn) or the native species Macrobrachium amazonicum (Amazon river prawn). The two hypothetical systems were compared using life cycle assessment (LCA) with the impact categories climate change, eutrophication, acidification, energy use, net primary production use, surface use and water dependence. Yields, species, feed conversation ratio (FCR) and feed processing were the factors with the most influence. The higher yield and lower FCR of giant river prawn induced lower impacts than native Amazon river prawn in all categories analyzed. Regardless of species, better effluent management in freshwater prawn farming, such as treating effluents with aquatic macrophytes or applying pond sediments to crops, significantly reduced eutrophication potential, making it extremely important to recommend using it in freshwater prawn farming.