A method and system for forming an in situ subsurface filter in a contaminated aquifer and for removing contaminants from groundwater drawn from a contaminated aquifer. The filter is produced in situ by injecting an aqueous solution comprising bacteria-stimulating chemical components through a well to bioactively generate a subsurface mineral filtering zone surrounding the well. As water is subsequently drawn through the well, contaminants are removed from the water as it passes through the filtering zone.