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As the core of arid Central Asia, Uzbekistan is experiencing prominent water scarcity with increasingly warming climate and accelerated human impact. To determine the hydrochemical characteristics and sources of toxic elements, as well as to assess water quality and health risks in Uzbekistan, 55 surface water samples were collected from the Amu Darya Basin of Uzbekistan (ADBU) and monitored for 20 parameters. A hierarchical cluster analysis showed that river water samples from the middle reach and Amu Darya Delta (ADD) were dominantly HCO3-Ca and SO4-Ca·Mg type, respectively. While the water samples collected near the former shoreline of the ADD and sewage outlets were dominantly Cl-Ca·Mg and Cl-Na types, which were consistent with the distribution of sites with high concentrations of toxic elements, seriously affected by human activities. Furthermore, principal component analysis indicated that the toxic elements of Pb and Cd in surface waters of the ADBU had industrial origins; local agricultural activities were considered to have contributed much of the NO3, Zn, Ni, Hg and Mn through pesticides and fertilizers; and Cu, Cr, As, and Co were controlled by mixed anthropogenic and natural sources. The results of water quality and health risk assessment also suggested that unsuitable drinking waters were displayed near the former shoreline of the ADD region and sewage outlets, and human health risks also occurred these areas.