Urbanization is rapidly occurring worldwide and can increase hydrological flows into urban streams and alter forest structure and soil properties. Stream restoration projects are ongoing in Fairfax County, Virginia in order to reconnect the channel to the floodplain and increase nutrient removal via microbially mediated processes. Ecological assessment of urban forests is also ongoing to understand the ecosystem services that urban forests provide. Using Illumina sequencing and qPCR, the bacterial and fungal communities were analyzed between stream riparian zones and reference sites, and between different forest qualities. Fungal communities differed significantly after stream restoration and between forest quality types. qPCR was also used to quantify denitrifying genes between restoration types. Post restoration sites had higher abundances of nirS, while reference sites were higher in nirK. The high quality forest sites were most colonized by arbuscular mycorrhizal fungi and were highest in ectomycorrhizal fungal sequences.