Decay kinetics of bacteria in biological wastewater treatment systems are vital to efficient design and operation of treatment plants.  Of special concern are decay characteristics of fecal indicator organisms, which can aid design of wastewater treatment processes to eliminate fecal pathogens.  This study focuses on characterizing the decay of three strains of the key fecal indicator bacterium, Escherichia coli, and comparing microbial techniques for quantifying decay rates.  Traditional metrics for monitoring decay include volatile solids and plate counts, which may not provide the full picture of specific decay dynamics. In particular, the viable-but-not-culturable growth phase is challenging to assay.  Recently, more specific molecular techniques have been developed, such as DNA and RNA extraction with qPCR and RT-qPCR, ATP assays and live/dead cell-staining.  However, these assays have not been widely accepted or bench-marked against traditional techniques.  It is expected that molecular assays will generate kinetic constants that better reflect the viability and activity of the bacteria as they decay, generating a more integrated understanding of the decay process.  Cells grown in pure culture were spiked into microreactors and subjected to a variety of time/temperature treatments in both buffered pure culture and sludge matrices.  These scenarios were intended to mimic on a small scale typical waste treatment processes, more specifically pasteurization, thermophilic digestion and land application.  Results indicate decay curves similar to traditional curves but with constants that vary with respect to the strains and the characterization methods used.  The foundation laid by this work can be utilized in further studies involving other organisms in a variety of environmental scenarios.