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The present study was aimed at understanding the impact of COVID-19 pandemic related restrictions on the freshwater aquaculture sector of Andaman and Nicobar archipelago (ANI). We interviewed the freshwater fish farmers ( N = 211) covering all the three districts (North and Middle, South Andaman, Nicobar district) of the archipelago. The results revealed the critical issues faced by the stakeholders such as fish seed unavailability, limitations in feeding, insufficient logistical support, movement related restrictions, lack of inputs, manpower shortages, etc. as the important constraints during lockdown. Our surveys also revealed that there was a significant reduction in the income of the farmers post COVID-19 outbreak ( p < 0.001). Possible reform strategies that could promote the sector development and resilience were outlined to recover from the COVID-19 impacts. The study also highlights the significance of effective networking among the stakeholders and necessary preparedness measures to be undertaken by the fish farmers to deal with the exigencies. The study also recommends a policy framework to strengthen the planning and management of freshwater aquaculture sector towards the path of sustainability.