Quartz sands contain various iron and clay minerals which coat silicate grains or are impregnated in silicate matrix. Treatment by basin water bioleaching in combination with electromagnetic separation can substantially improve the quality of quartz sands. The purpose of this in-situ study was to evaluate the feasibility of using a biological basin treatment process to improve the quality of quartz sands. The environmental conditions involved the changes of climate temperature, using fresh surface water without disinfection, inhibition of algae and fungi, and promoting bacteria. Analyses of the solution phase were used to monitor the dissolution of iron during the bioleaching of the quartz sands and to optimize the in-situ conditions for the bacterial activity. The rate of iron dissolution varied with environmental conditions, with the addition of nitriloacetic acid (NTA)/l and organic feedstock in the form of molasses. Bacterial removal of clay and iron minerals can be used to expose the white surfaces of quartz grains. The quartz sands from the Šaštín deposit (Slovakia) were used in glass industry after decreasing the Fe content.