Nitrous oxide is an important greenhouse gas and emissions from managed ecosystems are directly correlated to anthropogenic nitrogen input. Here we have measured nitrous oxide emissions from flooded depressions within croplands and from incubated soil samples. We scaled emissions to >20,000 comparable flooded depressions across Zealand in Denmark using a deep-learning approach based on aerial photos and satellite images. We show that flooded depressions within cultivated fields, representing less than 1% of the total cultivated area, can release 80 times more nitrous oxide compared to rest of the fields. Fluxes can remain high for more than two months after fertilisation and can account for 30 ± 1% of the nitrous oxide budget during that period. This highlights the urgent need for assessment of nitrous oxide hotspots, as managing these hotspots appear to represent an important part of the overall greenhouse gas emissions from managed croplands and an efficient mitigation action.