The agricultural input constraint such as irrigation, fertilizers, pesticides, fuel, and electrical energy are the key factors for increased water and carbon footprint values in atmosphere. Thus, optimal use of above mentioned farm inputs is highly needed for reduced environmental pollution. The CF and WF concepts provides a new comprehensive view, for the assesment of water and carbon footprints of onion crop cultivated under flodded and drip irrigation practices conducted at costal belt of Konkan region of Maharashtra state, India. The average CO2 emissions were computed as 22.30, 18.8, 20.46, and 20.01 t CO2 ha−1 under control, 0.8 ETC, 1.0 ETc, and 1.2 ETc irrigation scenarios, respectively. Irrespective of the growing seasons, the 1.2 ETc treatment resulted in highest onion yield (33.1 kg ha−1) among all the treatments, but with higher carbon emission rate. Whereas, the 0.8 ETc treatment was water efficient with minimum carbon emission rate, thereby forming a basis for achieving the optimal yield potential of the crop with a significant saving of water. The yield recorded during season 1 was higher by 22.8, 18.6, and 13.9% under 0.8 ETc, 1.0 ETc, and 1.2 ETc treatments, respectively, as compared to season 2. The emission rate of green WF was recorded to be significantly lower by 12.26, 23.63, and 26.97% under 0.8 ETC, 1.0 ETC, and 1.2 ETC, respectively, as compared to the control irrigation level. The higher values of green WF in control were mainly due to increased irrigation depth under flooded irrigation. The gray WF was also higher under control treatment as compared to rest of the treatments. The average CO2 emissions were recorded to be 22.30, 18.8, 20.4,6 and 20.01 t CO2 ha−1 under control, 0.8 ETC, 1.0 ETC, and 1.2 ETC irrigation scenarios. The irrigation treatment with highest amount of water application resulted in highest water and carbon footprint values, indicating an increasing trend from 0.8 ETc to 1.2 ETc during both seasons. The higher CF values in relation to irrigation were also correlated to increased water application and lower crop yields. Thus, drip irrigation coupled fertigation method may be the most possible way to reduce both WF and CF in relation to improved water and nutrient application to the crops.