Microbial communities are in close contact with the wetland soil microenvironment and can therefore function effectively as monitors of soil pollution. The objective of this study was to determine changes in the functional responses of microbial communities as a result of an external input of nutrients, while controlling for vegetation. A controlled experiment was performed at the mesocosm scale, consisting of two 1 m by 13 m raceways containing an organic peat soil, each planted with Cladium sp. and Typha sp. communities. One of the mesocosms was loaded with N (2 g N m −2 yr −1 ) and P (1 g P m −2 yr −1 ) for 18 mo. Nutrient loading resulted in increases in the soil and detritus labile nutrient pools, however, insufficient N and P where added to significantly alter their total levels. Over the experimental period, the extracellular enzyme acid phosphatase showed a significant decrease in activity across both plant communities ( P < 0.01) in contrast to β‐glucosidase activity, which varied primarily by plant community. Other microbial response variables such as the microbial activities (CO 2 and CH 4 production, P = 0.0016 and 0.0213, respectively), microbial biomass ( P = 0.0018) also varied primarily by vegetation type, with Typha sp. dominated areas exhibiting the highest level of activities. The nutrient dosing experiment indicated that the most immediate microbial response measures to nutrient enrichment are those directly associated to specific nutrients, such as P or N, while other measures showed a more complex response involving C source (e.g., vegetation type).