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Organic matter and nitrogen, crucial in terrestrial ecosystems, are limited in deserts due to the most obvious characteristics of scarcity of plant cover and low productivity. Little attention has been given to nutrient availability and ecological processes in desert sand dunes. We investigated the temporal and seasonal dynamics of carbon and nitrogen under two representative perennial shrubs of the Negev Desert inland sand dunes, Retama raetam and Artemisia monosperma. Having investigated total organic carbon, dissolved organic carbon, total soluble nitrogen, and mineralizable nitrogen in the soils at 0-10 cm depth, we conclude that in the Negev sandy soil ecosystem: (1) the concentration of carbon and nitrogen in the soil under the canopy of R. raetam was higher than in that under A. monosperma; (2) more available nitrogen appeared during the wet season compared to the other seasons, mainly due to regulation of soil water content; (3) the amounts of total organic carbon, total soluble nitrogen and mineralizable nitrogen were greatest in winter, and (4) nutrient heterogeneity is controlled mainly by plant cover rather than by the species forming the cover.