A method for treating (in situ) large bodies of water contaminated with heavy metals and having varying density stratas to immobilize the contaminant metals is disclosed. The method, or process for (in situ) immobilization of metals is focused on treating large bodies of water having metals therein that are also adjacent a border of soil or earthen materials in an attempt to immobilize the metals from penetrating through the soil. The method is also able to treat the soil water boundary within the pit lake to provide additional immobilization. The pit lakes can include open pit lakes, subterranean mine lakes, flowing streams and the like. The method is also able to treat an abandoned mine prior to the filling of the mine with water. Initially, the density mean of the body of water is determined, which is densest typical at regions at or approaching 4 degrees C. The process includes introducing a treatment substance that has a density greater than that of the density means into the body of water, providing at least one microbe proximate or in the body of water, producing microbial sulfides arising from the initial microbe placement, causing microbial sulfides to react (in situ) with metal ions or metal containing compounds located within the body of water, reducing the solubility of the metal ions by forming metal sulfides, and inhibiting the migration rate of the metal ions or other metal containing compounds within or from the soils or earthen materials as they settle out of the water.