The improvements in the existing methods of rapid detection and biological pathogen surveillance are still needed. The new spectroscopic methods that rely on the unique structural features and intrinsic fluorescence of microorganisms are well fitted for monitoring the spread of airborne biological agents or their reagentless detection in the air, and these methods may bring a new quality to bioaerosols remote detection. This review describes the problem of the confidence in the environmental testing results that may affect clearance standard, sampling techniques, and the estimation of risk of human exposure to the low concentrations of harmful microorganisms during bioterrorist event or naturally occurring outbreaks. Higher recovery efficiency of dangerous biological agents from the air and contaminated surfaces would enable more reliable environmental human risk exposure assessment.