Nitrous oxide (N2O) is a climate-relevant atmospheric trace gas. It is produced as an intermediate of the nitrogen cycle. The open and coastal oceans are major sources of atmospheric N2O. However, its oceanic distribution is still largely unknown. Here we present the first measurements of the water column distribution of N2O in the Gulf of Aqaba and the Red Sea. Samples for N2O depth profiles were collected at the time-series site Station A in the northern Gulf of Aqaba (June and September 2003, and February 2004) and at several stations in the central Red Sea (October 2014, January and August 2016). Additionally, we measured N2O concentrations in brine pool samples collected in the northern and central Red Sea (January 2005 and August 2016). In the Gulf of Aqaba, N2O surface concentrations ranged from 6 to 8 nmol L−1 (97–111% saturation) and were close to the equilibrium with the overlying atmosphere. A pronounced temporal variability of the N2O water column distribution was observed. We suggest that this variability is a reflection of the interplay between N2O production by nitrification and its consumption by N2 fixation in the layers below 150 m during summer. N2O surface concentrations and saturations in the central Red Sea basin ranged from 2 to 9 nmol L−1 (43–155% saturation). A pronounced temporal variability with significant supersaturation in October 2014 and undersaturation in January and August 2016 was observed in the surface layer. In October 2014, N2O in the water column seemed to result from production via nitrification. Low N2O water column concentrations in January and August 2016 indicated a significant removal of N2O. We speculate that either in-situ consumption or remote loss processes of N2O such as denitrification in coastal regions were responsible for this difference. Strong meso- and submesoscale processes might have transported the coastal signals across the Red Sea. In addition, enhanced N2O concentrations of up to 39 nmol L−1 were found at the seawater-brine pool interfaces which point to an N2O production via nitrification and/or denitrification at low O2 concentrations. Our results indicate that the Red Sea and the Gulf of Aqaba are unique natural laboratories for the study of N2O production and consumption pathways under extreme conditions in one of the warmest and most saline region of the global oceans.