Much is known about the positive effects of biosolids on crop production and quality, which mostly derive from the nutrients N, P and now S, plus indirect effects on soil structure and water holding due to the organic matter additions. However, less is known about microbial indicators of potential negative effects on soil fertility. These are difficult to evaluate for two main reasons: 1) lack of robust methods and 2) the difficulty of comparing assays based on microbial processes with those that relate to the structure and diversity of communities or individual populations. There is little evidence that C does not degrade at the metal concentrations likely in soils treated with biosolids. Turning to the nitrogen cycle, N-mineralization, nitrification and N₂-fixation have been examined in biosolids treated soils. The results are affected by the sensitivity of some of these processes to environmental factors such as pH (nitrification) and to methodological aspects of the assays such as the amount of substrate and time allowed for transformations. Less redundancy (fewer “species”) is involved in nitrification and N₂-fixation processes and this may behind the sensitivity of these processes. Symbiotic N₂-fixation, for example, in Rhizobium leguminosarum-clover systems is agronomically important. Numerous assays for soil microbial processes, community and population analysis exist, and many molecular methods are available. However, we still lack robust tests that are relatively unaffected by environmental variation and sufficient long-term experiments to use as platforms to study effects on long-term soil fertility. Until we have experimental resources that can be used and methods of linking population and community structure with activity we will not make much progress in understanding the effects of perturbations such as metals or other environmental stresses in soils. Legislators will meantime use indicators such as R. leguminosarum, or soil nitrification rate as sensitive indicators of potential change.