In wetlands it is still usual to use the same indicators of eutrophication which were developed to study the effects of nutrient enrichment in lakes; however, since hydroecology and biogeochemistry of wetlands is significantly different from lakes, monitoring of these indicators does not allow a good diagnosis of the changes undergone by the wetland ecosystem under nutrient enrichment scenarios. Microbial activities and their respective community responses have been considered as a measure of ecosystem stability and an indicator of ecosystem perturbation through changes on functional properties associated with nutrient cycling. As in most aquatic ecosystems, the addition of a limiting nutrient to wetland ecosystems promotes primary productivity and stimulates microbial processes. As nutrient loading increase, biogeochemical processes in wetlands are altered, changing their concentrations in water and soil, and therefore, nutrient fluxes and cycling. Nutrient enrichment induces changes in soil physicochemical and microbiological characteristics that may then serve as indicators of nutrient enrichment. In this review, a set of microbial community measurements known to be sensitive to nutrient enrichment in aquatic systems, such as extracellular enzyme activities, respiratory activities, microbial biomass C, N, and P, and microbially mediated N and P turnover rates have been used to characterize physiological response of the microbial community to wetland eutrophication. Some indicators as metabolic efficiency and phosphatase activity clearly reflect the main shifts on wetland ecosystem processes induced by nutrient enrichment and may be considered better than those that are currently used to assess the effects of eutrophication. Moreover, the combined use of different ecophysiological measurements such as extracellular enzymatic ratios and microbial biomass under resource allocation models and ecological stoichiometry demonstrates that ecophysiological measures are sensitive indicators of wetland eutrophication. Further studies are needed refining this approach to get the complex biogeochemical variability of the different wetland types, and to move from a sitebased heuristic model to a holistic approach, describing eutrophication patterns in wetlands.