Forest vernal pools experience strong environmental fluctuations, such as changes in water chemistry, which are often correlated with changes in microbial community structure. However, very little is known about the extent to which these community changes influence ecosystem processes in vernal pools. This study utilized experimental vernal pool microcosms to simulate persistent pH alteration and a pulse input of nitrate (), which are common perturbations to temperate vernal pool ecosystems. pH was manipulated at the onset and microbial respiration was monitored throughout the study (122 days). On day 29, was added and denitrification rate was measured and bacterial, fungal, and denitrifier communities were profiled on day 30 and day 31. Microbial respiration and both bacterial and fungal community structure were altered by the pH treatment, demonstrating both structural and functional microbial responses. The pulse increased denitrification rate without associated changes in community structure, suggesting that microbial communities responded functionally without structural shifts. The functioning of natural vernal pools, which experience both persistent and short-term environmental change, may thus depend on the type and duration of the change or disturbance.