Collectively, this design allowed us to examine more than just in-channel processes and provided two distinct mechanisms by which hydrology was manipulated. Natural hydrologic changes were hypothesized to disrupt microbial community structure and/or function resulting in variable denitrification rates. These differences were predicted to be more pronounced in the smaller stream, which experiences complete loss of flow, compared to the larger stream that maintained flow throughout the summer. We tested these hypotheses on seasonal/monthly time scales, which may provide insufficient resolution to see short-term changes. Thus we conducted an experimental manipulation to investigate short-term changes in Dabrafenib bacterial community structure and denitrification following inundation of riparian soils. Moisture content of soil, which is directly controlled by hydrology, plays a critical role in determining effectiveness of denitrification in NO3- removal. During times when it was flowing, LWD had higher denitrification rates than Sugar Creek and lower discharge. However, when LWD had no flow and was dry, denitrification rate dropped below that of Sugar Creek. Consistent with these findings, Pinay et al. determined that soil moisture was the most important factor in predicting rates of denitrification in streams with alternating flooding and drying cycles. When the dry sampling date at LWD is excluded, denitrification rates in LWD were much higher than in Sugar Creek. Prior studies demonstrate that NO3- is among the most potent environmental drivers of denitrification along with temperature and sediment organic matter content. In the present study, LWD had three times higher benthic organic matter than Sugar Creek and higher NO3- concentration. Likewise, in a study of these same streams, Baxter et al. found that LWD had higher rates of denitrification than Sugar Creek in summer. However, no significant differences between streams were observed in fall in that study, in contrast to the present study. In general, denitrification rates we observed are consistent with other studies of agriculturally impacted streams but rates in Sugar Creek were somewhat low, relatively, perhaps because of comparatively lower NO3- concentrations and higher discharge. At the same time that denitrification rates dropped in LWD with seasonal drying, total bacterial numbers declined perhaps because of elevated bacterial mortality or reduced growth. A lag period was also observed; bacterial cell numbers did not reach pre-drying levels until December, roughly one month following the return of stream flow. To examine the response of denitrifiers, nosZ gene abundances were examined because variation in denitrification potential within streams may be related to abundance of denitrification genes, while others have suggested that changes in abundance of the nosZ gene are a good predictor of N2O emissions. Overall bacterial community structure and denitrifier community structure had very similar patterns; T-RFLP profiles of both genes were strongly impacted by seasonal changes. Yet, differences between streams did not account for a significant portion of the variation in bacterial community structure.