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Previous studies indicated evidence of opportunistic pathogens in samples obtained during missions to the International Space Station (ISS). This study utilized TaqMan quantitative PCR to determine specific gene abundance in potable and non-potable ISS waters. Probe and primer sets specific to the small subunit rRNA genes were designed and used to elucidate overall bacterial rRNA gene numbers. In addition, primer-probe sets specific for Burkholderia cepacia and Stenotrophomonas maltophilia were optimized and genes of these two opportunistic pathogens quantified in the pre- and post-flight drinking water as well as coolant waters. This Q-PCR approach supports findings of previous culture-based studies however; the culture based studies may have underestimated the microbial burden of ISS drinking water.