Aquatic ecosystems around the globe face an increasing threat of eutrophication from algal blooms caused by excess nutrients. On Cape Cod, the major route for delivery of the limiting nutrient, nitrogen, to coastal ponds and estuaries is groundwater seepage. In 2005, researchers at the Woods Hole Marine Biological Laboratory installed and began monitoring a wood-chip based NITREX™ permeable reactive barrier (PRB) designed to remove nitrates via denitrification at the shore of Waquoit Bay, MA. In this experiment, I took groundwater samples from an array of multi-depth sampling wells within and surrounding the PRB. From each well I measured a suite of physico-chemical parameters and in a subset of samples I analyzed metagenomic DNA for the presence and abundance of the nirS nitrite reductase gene and examined the structure of the microbial community using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene. The PRB effectively reduced the nitrates from a maximum concentration of 109 μM in the core of the nutrient plume to below 10 μM inside and down-gradient of the PRB; however, a portion of the nitrate plume persisted at 3 meter depths underneath the PRB. Hydrogen sulfides present inside the PRB suggest seawater intrusion stimulates sulfate-reducing bacteria that may compete with denitrifiers for resources. Dissolved inorganic carbon (DIC) from respiration increased from 780 μM in the up-gradient groundwater to a maximum of 1985 μM inside the PRB. Dissolved organic carbon (DOC) increased from 8 μM in the inflowing up-gradient groundwater to a maximum of 130 μM in the PRB. High DOC concentrations extended down-gradient beyond the PRB. The presence and abundance of the nirS nitrite reductase gene, determined by PCR and qPCR, also increased inside and down-gradient of the PRB. DGGE results indicate the presence of distinct microbial communities among the sites. There was a high similarity between up-gradient PRB samples and control samples, with a different community emerging within the PRB, indicating that the PRB does have a measurable effect on microbial community composition.