To provide new insights into microbial functions in the Kushiro Wetland, Japan, we measured vertical profiles of fluorescein diacetate hydrolysis (total microbial activity), b-glucosidase and xylosidase (organic matter decomposition), acid phosphatase (phosphate production) and potential denitrifying (denitrification) activities as microbial enzyme activities in soil to depths of approximately 1.5 m from two sites with different vegetation in November 2008 (winter) and August 2009 (summer). Active organic matter decomposition, phosphate production and denitrification were evident in shallow litter and peat layers, and total microbial activity was high. Almost no differences in decomposition and total microbial activity were observed between seasons, whereas phosphate production and denitrification were higher in summer. All activities were low in mid-depth volcanic-ash and clay layers because of low carbon, nitrogen and phosphorus levels. Surprisingly, the total microbial activity and decomposition in deep clay & peat and peat layers were the same as or higher than in shallow layers. However, denitrification was limited, probably because dissolved organic matter containing humic-like substances was unsuitable as a substrate. Moreover, total soil phosphorus levels, acid phosphatase activity and multiple linear regression analysis revealed that the soil in the Kushiro Wetland is likely P limited.