Denitrifying up-flow packed-bed bioreactors fed with perchlorate and nitrate allowed for the examination of the impact of a variety of salt conditions (up to 10% w/v NaCl) on the complete perchlorate and nitrate removal capacity of the reactor using activated sludge taken from a municipal wastewater treatment plant. Based on the evaluation of the microbial community in the bioreactor by cloning analysis, Clostridium sp. and a Rhodocyclaceae bacteria were identified as the dominant clones. This suggests that they may be tolerant to high salt and can reduce both nitrate and perchlorate in such conditions.