The use of biological indicators to monitor the health and functioning of wetlands has been an ongoing goal of wetland scientists and managers, and has focused primarily on monitoring the changes in macroorganisms, due to the relative ease of identifying and counting them. In recent years, the establishment of high-throughput sequencing techniques, development of assays for specific functional genes, and better quantitative measures are making it easier to get extensive diversity profiles and more robust abundance estimates of various microbial communities, and empowers us to explore wetland microbiomes and their role in ecosystem function. This heuristic search enables us to illuminate a spot light on minor populations of microbial communities, which were difficult to be scrutinized by more traditional molecular tools. Monitoring microbial indicators in response to nutrient loading, pollutants and redox potential is beneficial for wetland ecosystem management. Microbial populations can serve as the most sensitive and rapid bioindicator in response to various environmental changes. Evaluation of wetland condition and restoration cannot be met effectively by a single physical, chemical or biological parameter but a combination of multiple attributes is effective for robust wetland assessment and management. Various functional groups of microorganisms can be used as wetland assessment tools and provide a more profound understanding of microbial population dynamics and various direct microbial activity measurements. Understanding of the microbial communities controlling biogeochemical cycles in constructed wetlands could support optimizing performance of these promising treatment systems. This review focuses on a potential use of microorganisms as effective biological indicators for wetland management.