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Worldwide aquaculture production is increasing at annual rates of 5–11% to meet the global increase in animal protein demand. While aquaculture can be an important means for poverty alleviation and food security in poor regions, the aquaculture boom also comes with environmental costs. In ~100 aquaculture ponds in different climate regions in Brazil we will quantify greenhouse gas emissions (methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O)), construct nutrient (nitrogen, phosphorus and carbon) budgets and conduct life cycle analyses. Different management practices will be compared, with the ultimate goal to contribute to the development of an overview of best-practices.