Mass balance calculations and analysis of the redox species in the aqueous and solid phases are used to assess the behavior and removal rates of the oxy-anions of arsenic, selenium, and molybdenum during primary sedimentation, activated sludge, and anaerobic digestion processes of three full-scale wastewater treatment plants (WWTPs). The dominant form of the oxy-anion found in any treatment system was, to a large extent, controlled by slow oxidation rates and interactions at solid-water interfaces. The removal of the oxy-anions of the three elements was limited by the form in which they were loaded into the WWTPs and by internal recycling processes. Under anaerobic conditions, the formation of stable sulfide, organic and carbonate (with arsenic only) complexes resulted in significant release of the elements from the solid phase back into solution. Formation of volatile compounds resulted in the loss of up to 50% of the selenium loading into one facility, suggesting that WWTPs may be a significant source of selenium emitted to the atmosphere.