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Migratory birds face numerous challenges as they travel to and from their wintering grounds. Their ability to overcome these obstacles depends on their physical fitness, energy reserves and migration strategy. During migration, birds often need flight interruptions in vegetated areas which play a crucial role for migrants heading to wintering quarters or flying back to breeding areas. For the migratory raptor, the Western Marsh Harrier Circus aeruginosus a particularly difficult challenge is crossing the Sahara Desert. In this region, the birds encounter areas with lack of vegetation and harsh atmospheric conditions. To understand their behaviour in such an unfavourable environment, we studied the migratory patterns of Marsh Harriers in the Sahara Desert using GPS/GSM telemetry from 2019 to 2023. We examined flight interruptions within an hourly resolution and unique stop sites in hyper-arid areas of the Sahara Desert and enhanced the dataset with Normalised Difference Vegetation Index (NDVI), land cover data, U (velocity of the east-west) and V (velocity of the north-south) wind components and sunrise and sunset times. We explored the timing of the daytime flight interruptions used by Marsh Harriers and described the selection of sites with emphasis on the NDVI. Marsh Harriers preferred areas with higher NDVI and increased distance between unique stop sites. We also found increased density of flight interruptions during late afternoon and tendency for flight interruptions in the vicinity of consecutive night roost. Flight interruptions were also affected by wind conditions. Our study, made possible by advanced GPS/GSM technology and remote sensing data, provides new insights into the use of unique stop sites by Marsh Harriers during migration over the Sahara Desert. It underlines the importance of scarce vegetation during the Sahara crossing for the Marsh Harrier and helps to explain the selection of areas within a harsh environment used for breaks of a short duration. Our findings open the door for further investigation of Marsh Harrier behaviour during migration through harsh environments.