The functional importance of bacteria and fungi in terrestrial systems is recognized widely. However, microbial population, community, and functional measurement endpoints change rapidly and across very short spatial scales. Measurement endpoints of microbes tend to be highly responsive to typical fluxes of temperature, moisture, oxygen, and many other noncontaminant factors. Functional redundancy across broad taxonomic groups enables wild swings in community composition without remarkable change in rates of decomposition or community respiration. Consequently, it is exceedingly difficult to relate specific microbial activities with indications of adverse and unacceptable environmental conditions. Moreover, changes in microbial processes do not necessarily result in consequences to plant and animal populations or communities, which in the end are the resources most commonly identified as those to be protected. Therefore, unless more definitive linkages are made between specific microbial effects and an adverse condition for typical assessment endpoint species, microbial endpoints will continue to have limited use in risk assessments; they will not drive the process as primary assessment endpoints.