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Groundwater is all important and often exclusive water resource in and and semi-arid regions. The aim of the present paper was to gain insight into the processes and conditions that control the deterioration of groundwater quality in the semi-arid Kalahari of Botswana. Measurements of He-3, He-4, Ne-20, Ne-22, and of C-14 of dissolved inorganic carbon (DIC) were combined with existing isotopic and hydrochemical data to investigate groundwater from the Ntane Sandstone Aquifer, which is affected by high nitrate concentrations of non-anthropogenic origin. All groundwater samples revealed neon concentrations in excess to air-saturated water, which we attributed to the addition of excess air during recharge. Neon concentrations ranged from values close to air saturation for C-14 DIC rich samples (up to 80.5%MC) up to values of 90% in excess to air-saturated water for lower C-14 DIC contents (2.6 61.3%MC). A strong linear correlation of excess Ne with nitrate concentrations suggests an intimate connection between groundwater quality and the processes and conditions during groundwater recharge. Low groundwater recharge rates under present-day semi-arid conditions are associated with low amounts of excess Ne and elevated nitrate concentrations. In contrast to this, higher excess Ne values in groundwater of lower C-14 DIC and nitrate contents indicate that the high quality groundwater end-member presumably is related to higher groundwater table fluctuations during wetter climatic conditions in the past. We attribute the decline in groundwater quality with respect to nitrate to a decreasing rate and temporal variability of groundwater recharge, and to concurrent changes in biogeochemical activities following a transition to a drier climate during the Holocene. Under such conditions, a much stronger decrease in groundwater recharge compared to the release of nitrate from soil organic matter may result in elevated nitrate concentrations in the vadose zone and groundwater. This implies a strong impact of climate change on the transport of solutes like nitrate through the vadose zone which needs to be considered in predictions of future groundwater quality. (C) 2008 Elsevier Ltd. All rights reserved.