The inventive process scheme and its various embodiments described herein will comprise filtering a selenium containing water by reverse osmosis or nanofiltration to produce a primary permeate stream at least meeting the water stream effluent discharge requirements of the location and a concentrate stream containing the removed selenium and other species, a RO or NF concentrate treatment specific to the case which will treat and reduce the selenium content of the concentrate, optionally in conjunction with a sulfate removal process, and result in a highly concentrated sludge or other output, and a selenium depleted aqueous overflow stream, a portion of which will be combined with the primary permeate stream so that the selenium content of the combined stream does not exceed the local requirement, and the reminder of the selenium depleted aqueous overflow stream will be returned to be combined with the selenium containing water entering the inlet of the primary reverse osmosis treatment.