The present invention discloses a novel microbial process for decontaminating (per)chlorate and/or nitrate containing matrices. A heterotrophic mixed microbial culture expressing the functional genes responsible for (per) chlorate and nitrate reduction is the major component of the process. The present process can be a better substitute for existing processes for decontaminating perchlorate contaminated propellant wastewater, ion exchange resin/regenerate solutions, etc. The consortium consists or comprises of Halomonas sp. NIIST-PRB-02 (MTCC No. 5911), Bacillus sp. NIIST-PRB-03 (MTCC No. 5912) and Serratia marcescens strain NIIST5 (MTCC No. 5821).