Nitrate leaching from agricultural systems poses a threat to ecosystems and human health. Integrating 2D carbon-based graphite nano additive (GNA) soil amendments previously demonstrated potential in mitigating nitrate loss, yet the responsible mechanism was unclear. To clarify the causal mechanism, this dissertation aimed to identify and understand mechanisms of how addition of graphite nano-additive (GNA) soil amendment reduces N leaching through agricultural soil by sequential investigation employing laboratory soil incubation tests, batch adsorption experiments, soil column experiments, and greenhouse pot study. Soil incubation tests were conducted with four commercially available graphene nanomaterials to establish that soil microbial activity indicated by respiration was significantly enhanced when soil was amended with graphene (e.g., GNA). Additionally, gene abundance assessment from the same incubation tests indicated a potentially slowed soil nitrification (ammonium to nitrate conversion) by GNA. Separate batch absorption tests indicated that GNA was unlikely to retain nitrate through adsorption. Soil column experiments were designed to probe the dependency of N retention in GNA-amended soil primarily due to altered microbial activity from assessing the impact of temperature, soil saturation, sterility, hydraulic retention time, GNA dose, and soil organic carbon. Finally, a greenhouse plant growth study was designed to assess how GNA impacts soil biology. Enzyme activity indicated GNA could stimulate soil carbon mineralization and improve soil bioavailable carbon. Gene abundance assessment showed total bacterial community size was unimpacted but selected and suppressed certain bacterial groups (e.g., suppressed bacterial amoA gene abundance).16S bacterial community sequencing showed that GNA significantly altered the bulk and rhizosphere soil microbiome composition. GNA-induced selection of certain bacterial classes (e.g., Bacilli) holds significant implications in aspects of plant growth and nutrient acquisition. This dissertation revealed mechanisms behind GNA-induced decrease of nitrate leaching in agricultural soil, aiding progress to its integration into conventional agriculture to improve nitrogen fertilizer efficiency for a food-secure future.