The present invention relates to methods, compositions and systems for detecting perchlorate in a sample. Compositions useful for detecting perchlorate in a sample include those comprising a perchlorate reductase, a reductant and an electron shuttle. In an exemplary embodiment, the composition comprises perchlorate reductase from Dechloromonas agitata, reduced nicotinamide adenine dinucleotide and N-methylphenazinium methylsulfate. The present invention also provides for methods of using the compositions disclosed herein, as well as systems thereof. In some exemplary embodiments, the methods comprise a concentration step, in which, for example, the sample is contacted with a cationic solid phase extraction column. Employing this step provides certain advantages such as a lowered detection limit and the removal of contaminants.