This study presents an assessment of the potential application of Mn content in rock varnish laminae as a paleoclimate indicator. To investigate the environmental controls on varnish formation, we determined Mn composition in rock varnish formed on flint artifacts produced during the earliest Holocene from eight coeval prehistoric sites in the Negev desert, Israel. These sites lie along a north–south annual rainfall transect ranging between 120 and 30 mm yr− 1. The varnish is ~ 100 times enriched in Mn relative to the content in the desert dust source material. Chemical profiles across the varnish display 4–6 distinct Mn peaks in all sampled sites, pointing to systematic fluctuations within the varnish along a wide range of environmental settings. The mean Mn contents in the various sites range between 10.7 and 15.6 at.%, yet within this range, the Mn content in the Negev varnish does not show a correlation with mean annual rainfall. As moisture is needed for Mn mobility, wetting cycles by dew or light rain, which are not adequately represented by the mean annual rainfall amounts but control the number of wetting–drying cycles may explain the variance within the results from the arid and hyperarid Negev varnish.