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Although the environmental footprint of cattle and poultry have been well documented in the Amazon, resultant greenhouse gas (GHG) emissions and land use intensities of the expanding aquaculture are poorly understood. Moreover, we know little about whether emissions vary in aquaculture ponds dominated by different fish species, such as Colossoma macropomum (tambaqui), the most common cultured species in the Amazon, and Arapaima gigas (pirarucu). Differences among fish species in feeding modes, morphology, and habitat use could strongly influence GHG emissions. Additionally, land use change may have far-reaching consequences for the net GHG footprint of aquaculture systems. However, land use change emissions have been largely overlooked in aquaculture sustainability assessments. Here we investigate the GHG emissions from fish ponds and GHG emissions associated with land use change due to aquaculture expansion in the Southern Amazon region, where large fish farming operations have been implemented to meet increases in the local and regional demand for fish. In addition, we investigated how GHG emissions of Amazon aquaculture compare to cattle production systems. To estimate the direct GHG emissions from fish ponds, we surveyed 45 fish ponds in Rondônia State, Brazil, and collected diffusive and ebullitive GHG emissions. GHG emissions from land use change were estimated by mapping fish farm locations using deep learning, and evaluating the historical trajectory of the land cover of each mapped pond. After, we used standard techniques proposed by the Brazilian National Inventory to estimate GHG emissions due to land use change. GHG emissions from fish ponds in the Southern Amazon varied from 2.3 to 8.0 gCO2eq m-2 d-1. Total GHG emissions from aquaculture ponds did not significantly differ among fish species, regardless of differences in species traits such as body size and feeding mode. We conclude that management strategies rather than fish species are the primary driver of variation in GHGs emitted from fish ponds in the Southern Amazon. Although we observed substantial carbon loss to the atmosphere, the GHG emissions from aquaculture are 2 to 3-fold lower than that emitted from cattle per unit of live weight produced.