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Microorganisms such as Cryptosporidium are enumerated by techniques that are susceptible to considerable losses, resulting in highly variable recoveries. This research quantified the methodological uncertainties in microbial concentration and removal data to demonstrate the effects of organism count, sample volume, replication, and methodological recovery on methodological uncertainty in microbial data. The authors found that the uncertainty associated with microbiological methods is more substantially reduced by increasing organism count to 10 or more than by improving methodological recovery. This investigation demonstrates the necessity of treatment technique-based regulations such as the Long Term 2 Enhanced Surface Water Treatment Rule. Findings further suggest that before revisions to the Total Coliform Rule are finalized, a rigorous quantitative analysis should be conducted of the uncertainty associated with compliance data derived from the rule's approved analytical methods. Includes 36 references, figures.