A biological system for removing selenium from waste water comprises a first immobilized cell bioreactor (ICB) and a selenide removal module. The first ICB comprises a chamber having a substrate housed therein and situated to contact the waste water flowing therethrough during use. Anaerobic microorganisms are supported on the substrate, and comprise selenium respiring bacteria capable of reducing selenates and selenites to insoluble elemental selenium and/or sulfate reducing bacteria capable of reducing selenates and selenites to insoluble elemental selenium or to soluble selenides. The selenide removal module includes metallic or oxidized iron compounds capable of chemically reacting with selenide or sulfide compounds in the waste water to form iron selenide or iron sulfide precipitates.