Soil microorganisms are pivotal in ecological systems, it may not be possible to define an ecosystem where an impact on overall microorganism populations would not mean a severe impact on the ecosystem. They are as relevant to an ecosystem as any group of organisms could be. At the same time, it is very difficult to link impact on measurable microbial activities to ecological impacts. We lack the required understanding. The linkage fails because of: compensation processes—the ecological process is continued by organisms other than those measured; non-specific assays—the method used to measure activity may impose conditions that do not reflect ecological conditions and multiple and unknown interacting factors. Overall, the ambiguity in benefit/ detriment relationships for impacts on microbes is the largest problem. Here we describe several examples of successes and failures of soil microbial bioassays in applications related to soil cleanliness criteria and ecological risk assessment. The usefulness of the microbial bioassays remains in question.