The most promising technologies to remove perchlorate from water are ion exchange and biological reduction. Although successful, ion exchange only separates perchlorate from water; it does not eliminate it from the environment. The waste streams from these systems contain the caustic or saline regenerant solutions used in the process as well as high levels of perchlorate. Biological reduction could be used to treat the regenerant waste solutions from the ion exchange process. A treatment scheme, combining ion exchange and biodegradation, is proposed to completely remove perchlorate from the environment. Perchlorate-laden resins generate brines containing salt concentrations up to 6% or caustic solutions containing up to 0.5% ammonium. Both, high salt and ammonium hydroxide concentrations are potentially toxic to microorganisms. Therefore, the challenge of the proposed system is to find perchlorate reducing microorganisms that are effective under such stressful conditions. Preliminary results have shown that salt concentrations as low as 0.5% reduced the perchlorate biodegradation rate by 30%; salt concentrations greater than 1% decreased this rate to 40%. Although biodegradation was seen in ammonium levels of 0.4%, 0.6% and 1%, the perchlorate biodegradation rate was 90% of that at 0% ammonium hydroxide. Further research will focus on the isolation and/or acclimation of microorganisms that are able to biodegrade perchlorate under these stressful conditions.