Meteorological conditions influence strongly the energy and water budget of birds. By adjusting their flights spatially and temporally with respect to these conditions, birds can reduce their energy expenditure and water loss considerably. By radar, we quantified songbird migration across the western Sahara in spring and autumn. There autumn migrants face the trade-off between (a) favorable winds combined with hot and dry air at low altitudes and (b) unfavorable winds combined with humid and cold air higher up. Thus, it can be tested whether birds may chose altitudes to minimize water loss instead of energy expenditure. We predicted optimal flight altitudes with respect to water loss and energy expenditure based on a physiological flight model when crossing the western Sahara and compared these model predictions spatially and temporally with measured songbird densities. The model aiming for minimal water consumption predicted a mean flight altitude of 3,400 m under autumn conditions. However, 64% of the nocturnal songbird migration flew at altitudes below 1,000 m above ground level profiting from tailwind. This preference for tailwind in autumn, despite the hot and dry air, emphasizes the importance of energy savings and diminishes the significance of possible water stress for the selection of flight altitude. Nevertheless, during daytime, high energy expenditure due to air turbulences and water loss due to warmer air and direct solar radiation prevent songbirds from prolonging their nocturnal flights regularly into the day. Birds crossing the Sahara save water by nocturnal flights and diurnal rests.