This study was conducted to determine the effects of the waste-rock dump (WRD) of the underground polymetallic Balya Mine on the Kocacay River and eventually on Lake Manyas in Turkey. Data presented in this paper include geochemical characteristics of various kinds of water (mine, surface and groundwater) and of suspended-particle samples in the vicinity of Balya. The more polluted mine waters have low pH and high conductivity, while high concentrations of Zn, Cd, Mn tend to be found in the dry and wet seasons. High concentrations of Pb, As, Cr, Cu and S appear only in the wet season. The sources of the heavy metal concentration within the Kocacay River are leached waste, surface run off, and overflow from the spillway of the WRD. To minimize the formation of acids and dissolved metal, and for the remediation of the harmful effects of extreme contamination conditions, it is recommended that lime or alkali materials and organic carbon be added to simulate the action of sulfate-reducing bacteria.