Dave, As I understand your ...

Dave,

As I understand your question, you are looking for more natural, non chemical, non mechanical methods for removing these contaminant from a lake, pond, stream or groundwater aquifer.  That is a difficult if not impossible task to accomplish. Most of the contaminants you mentioned are naturally occurring in some mineral deposits and as a result leach into water sources with runoff, acid rainfall and normal groundwater percolation.

You can't simply destroy the metals, so to remove them requires some type of coagulation, precipitation or absorption onto another media.  For a surface water body, a constructed wetland with carefully selected plants may be the best answer to take advantage of bio-absorption /metal uptake by the wetland plants. At the end of the day though the plants would have to be harvested to remove the metals and the biomass disposed of somewhere, preferably a secure landfill where they won't find their way back to water.    I'm not selling anything, just my thoughts on the subject. Good luck,  Bob Duff