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Floods along arid ephemeral streams are considered as the major source of groundwater recharge into the shallow alluvial aquifer, which is served as an intermediate sub-surface storage for deep percolation and recharge into deep regional aquifers. Contaminants accumulated in the upper basin reaches, might be transferred by floods and spread along the riverbed shallow aquifer. The longitudinal flux along the alluvial aquifer and mixing with local water control. the spatial distribution of the groundwater pollution. Anthropogenic pollutants and industrial contaminants had been accumulated in the upper Beer shiva wash in the northern Negev desert, Israel. A multi-variable cluster analyses performed on dissolved chemicals and environmental isotopes in the shallow groundwater were used to discretize the alluvial aquifer into hydrological compartments. A multi-cells mixing cell model was applied to identify and quantify sources of recharge, rates of streambed infiltration, and longitudinal fluxes along the shallow alluvial aquifer. Results elaborated on the role of floods in transmitting the pollution along the graveled-bed aquifer.