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Regions of rainfall gradients at desert margins are areas where eco-geomorphic changes and degradation in response to global warming and grazing are most intensive. Assessment and understanding of the consequences of global warming and human disturbance of these vulnerable ecosystems requires detailed information regarding the spatial variation of soil and vegetation properties and their dependence on rainfall. Such detailed information is still of limited availability. This study aimed to rectify this shortcoming by analyzing data on the chemical and spectral properties of soil samples collected along the Judean Desert climatic gradient. Six clusters of typical chemical soil properties were identified. Dependencies of clusters’ chemical properties (total iron, organic and inorganic carbon) on annual rainfall amounts were found to be significant. Two spectral Landsat TM band ratios introduced to assess soil conditions showed significant correlations with these chemical properties. These ratios were found to be higher correlated than individual chemical properties with average rainfall suggesting that spectral data may represent a broader range of chemical, physical, and biological site properties. Examining the three-way relationships between soil chemical properties, their spectral reflectance characteristics and rainfall, facilitates a better understanding of the generalized trends along the climatic gradient and more specifically of modes of transition from semi-arid to arid zones.