The present study was conducted to determine the carbon (C) footprint of different aquaculture production systems in India. The total input (kg CE/ha) in different cultures, respectively, was 1,811 to 4,144 for scampi, 4,417 to 5,913 for polyculture, 4,090 to 8,873 for shrimp and 2,417 to 2,786 for carp. Of the total inputs, feed accounts for around 90% of carbon equivalent (CE), in all cultures. The output in different cultures, expressed on live weight basis (kg/ha) and on input basis (kg/kg), respectively, was 1,280 to 3,288 and 0.71 to 0.79 for scampi culture, 4,639 to 5,998 and 1.00 to 1.05 for polyculture, 2,130 to 5,436 and 0.52 to 0.61 for shrimp culture, 4,100 to 4,160 and 1.49 to 1.70 for carp culture. On the basis of output:input ratio, the carp (three species of Indian major carp) culture is more sustainable followed by polyculture (carp with scampi), scampi and shrimp culture, respectively.