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Lake Ngami in semiarid Botswana was dry until 2009 when it began filling with water because of regional increases in precipitation and from redirection of water to the lake from distributaries of the Okavango River. We measured the physical, chemical and stable isotopic composition of lake water collected at 25 cm below the surface along a 18 km axial transect from the inflow river to the distal end of the lake. Our objective was to determine the processes that control water properties and to establish baseline values for future temporal and spatial comparisons. The major ionic concentrations (e.g., Cl-, Na+, Ca2+) and the stable oxygen (delta O-18) and hydrogen (SD) isotope ratios show three distinct regions of increasing concentrations and isotopic enrichment, respectively along the transect. The delta O-18 vs. SD data plot along the Okavango Delta evaporation line and suggest modification of lake water by evaporation. The proportions of the major ions in the inlet water and in the lake were similar and logCl(-) vs. logNa(+) suggests an evaporative enrichment of solutes. The segmentation of the major solutes and the delta O-18 and SD into three regions along the axial transect results from differential evaporation of lake recharge from 2010, 2011 and 2012, and are thus controlled by the residence time of recharge in the lake. Unlike the major ions, the dissolved inorganic carbon (DIC) concentrations and the stable carbon isotopic ratios (PC) of DIC increase along the axial transect to about midway in the lake, and then reach steady state. The delta C-13 of dissolved organic matter in the inlet river and lake averaged similar to-25.7 +/- 0.3 parts per thousand while that for particulate organic carbon decreased from similar to-24 parts per thousand in the inlet river to similar to-28 parts per thousand in the lake from water column productivity. Carbon cycling in Lake Ngami is controlled by evaporation which increase DIC concentrations and equilibration between carbon in DIC and atmospheric CO2(g). The results show the importance of evaporation and residence time in controlling the solute chemistry and the dominance of atmospheric CO2(g) in controlling carbon cycling during the filling stages of lakes in arid environments. (C) 2015 Elsevier B.V. All rights reserved.