Woodchip bioreactors (WBRs) are an emerging low-cost, passive systems for nonpoint source nitrogen (N) removal via denitrification at terrestrial−aquatic interfaces. With approximately one-quarter of applied N amendments crossing a land-water boundary prior to discharge to receiving waters, these edge-of-field applications provide an ideal opportunity for agricultural wastewater treatment. However, concerns regarding the longevity of these systems – particularly declining labile carbon release from lignocellulosic support material over time – are an impediment to their widespread adoption.Recent research has identified the implementation of drying rewetting (DRW) management strategies increases dissolved carbon concentrations within reactor porewater and is accompanied by increased removal rates of nitrate, a beneficial outcome for protecting downstream water quality. The impact of these induced oxic-anoxic cycling regimes has not been examined in the context of greenhouse gas (GHG) emissions though, particularly in regard to nitrous oxide (N2O), a potent greenhouse gas and intermediate of the denitrification pathway. This dissertation seeks to disaggregate physical, chemical, and biological controls on N dynamics within WBRs to better comprehend N2O transformation and fate to improve design and operation of the next generation of green infrastructure. Three projects were undertaken to assess the potential for tradeoffs between limiting aqueous N concentrations at the expense of increased GHG emissions. The first project coupled a multi-phase advection-dispersion model and computed microtomography to quantify entrapped gas phase volumes within woodchip media subject to DRW regimes. Variable water tables led to greater bubble entrapment – which can inhibit denitrification and sequester produced GHGs, leading to “hot moments” of mass release later when water levels fall. The second project assessed coupled carbon-nitrogen flows within WBRs under oxic-anoxic cycling and revealed that DRW cycles increase nitrate removal without concurrent accumulation of N2O – contrary to conventional conceptions of denitrification. The third project sought to explain these unexpected results through an investigation of the microbial community. Preliminary metagenomic sequencing suggests no significant shift in the functional or taxonomic identity of WBR microbiology under DRW conditions, and forthcoming metatranscriptomics suggest observed chemical profiles may be explained by changes in gene expression levels. Overall results imply that DRW is a beneficial management strategy for WBRs.