Degradation of water quality due to nutrient over-enrichment has become a global environmental concern. In Aotearoa, agricultural pollution of freshwaters by nutrients is increasing. Therefore, strategies need to be implemented to minimize nutrient pollution in surface waters. Denitrifying bioreactors (DBRs) are a prominent edge-of-field treatment technology to mitigate surface water nitrate loadings from agricultural subsurface drainage. Recent studies have identified that subsurface drainage can also contribute to the loss of phosphorus from agricultural soil. Therefore, this thesis investigates the potential of DBRs to incorporate iron-based materials to sequester phosphorus and reduce pollution of waterways. There is some evidence suggesting low-level phosphorus removal by woodchip bioreactors alone. However, it is inevitable that woodchips alone do not abiotically remove phosphorus due to the incompatibility between the surface charge of wood at neutral-to-acidic pH values. In this study, raw pinus radiata, and, thermally modified pyrolyzed woodchips were employed for surface modification, with view to enhancing P binding in DBRs. We were mindful in the design of material functionalization to avoid complicated preparation steps, exotic or harmful reagents, and impractical particle sizes to ensure compatibility for large-scale applications in the agricultural landscape. Results indicated that the functionalization of wood media successfully inversed the surface charge, leading to a net positive charge within the favorable range for phosphorus adsorption under reactor-specific conditions (pH 5.5 − 6). The maximum adsorption capacity of functionalized wood and functionalized biochar corresponded to 65.8 mg g-1 and 31.4 mg g-1, respectively, comparing well to values reported in the literature. DBRs operate under varying hydraulic conditions, which results in variable flow rates, nutrient concentrations, redox status, pH, and many other variables that affect the operation of the bioreactor. The stability of iron hydr(oxide) composites is expected to be sensitive to some of these conditions, especially acidic and anaerobic conditions, which favor dissolution of iron hydr(oxide)s and therefore could adversely affect P removal. Furthermore, there are other likely products of reduced Fe2+ and orthophosphate (HPO42-) that could form under the conditions anticipated. Therefore, the biogeochemical environment in the DBR was characterized to understand the stability of iron hydr(oxide)s and their ability to subsequently remove of phosphorus. To date, there have been only limited investigations into the stability of iron hydr(oxide)s under real-world bioreactor conditions, and functionalisation studies often neglect the impact of oscillating redox conditions on the stability of Fe-based adsorbents. In light of this, bench-scale woodchip bioreactors were established, both with and without MnO2, to evaluate the redox buffering capacity of MnO2 with view to mitigating the reductive dissolution of iron oxide. This approach aimed to improve the retention of dissolved reactive phosphorus (DRP) on the introduced iron oxide surfaces. It was concluded that iron oxides effectively remove DRP and MnO2 enhances nitrogen (N) removal, with slightly better performance observed in the treatment incorporating Fe oxides and MnO2. Hence, it can be inferred that the addition of manganese and iron oxides proves advantageous as an amendment to the conventional woodchip substrate in DBRs to enhance nutrient removal. This thesis has demonstrated that Fe-functionalized media can effectively remove DRP in agricultural drainage water. In addition, by incorporating MnO2, Fe oxides can be stabilised under oscillating redox conditions, and therefore the combination of MnO2 and Fe oxides could serve as a practical solution for DBRs to mitigate diffuse pollution in New Zealand. These findings offer insights for redesigning DBRs, providing a clearer understanding of the dynamics of P removal in DBRs, and how functionalized media can be employed in the long term to remove phosphorus from agricultural drainage water, meeting water quality objectives while minimizing P releases.