Contamination of water and sediments with arsenic and heavy metals is a global issue affecting human health. Regions covered with Quaternary deposits have received little attention from the point of view of the flux of arsenic and heavy metals from sediments to surface water. This study aims to determine the flux of arsenic and other heavy metals from Quaternary sediments to surface waters in an area affected by the former Złoty Stok gold and arsenic mine. Contamination in surface waters and sediments was caused by arsenic, whereas concentrations of metals were usually within water quality standards. Arsenic contamination of surface water increased in the lower part of the basin covered by Quaternary sediments, and exceeded water quality standards by 2 orders of magnitude. Arsenic mass flux exceeded 8 kg/day near the confluence of the Trująca River with the Nysa Kłodzka, a main tributary of the Oder River. An increase in arsenic concentration in the lower part of the basin is related to mine tailings and preferential flow of groundwater through Quaternary sediments. In future, water resources scarcity may lead to an increase in arsenic contamination in surface and groundwater.