Biogeochemical dynamics of manganese (Mn) and iron (Fe) in redox-dynamic environments play important roles in regulating water quality in natural and nature-based systems. Manganese is a contaminant of concern in drinking water systems, and its mobilization and speciation in redox-stratified water columns is regulated by hydrological patterns that are changing in a warming climate. Interactions between Mn or Fe oxide minerals and organic matter can play an important role in either stabilizing or destabilizing organic carbon, depending on the redox state and transformations of Mn and Fe, with implications for the bioavailability of carbon to fuel microbial activity in denitrifying bioreactor systems. The work described in this thesis integrates field-scale observations, geochemical modeling, and multi-modal synchrotron techniques to elucidate how redox-dependent dynamics of Mn and Fe influence water quality in systems including drinking water reservoirs and denitrifying biofilter systems. In a weakly stratified drinking water reservoir, prolonged stratification during drought conditions was found to enhance manganese release, complicating treatment process. We monitored Mn in the Ithaca Reservoir during two contrasting years: a wet year in 2021 and a dry-to-moderate drought year in 2022. The results showed that decreased streamflow during the dry year increased stratification and raised Mn concentrations in the hypolimnion. The contrasting conditions allow us to study how stratification impacted the mobilization and precipitation pathways for Mn and we found that mixed calcium-manganese carbonates, rather than MnCO3, may contribute to Mn cycling. These findings emphasize the role of hydrological and geochemical interactions in controlling manganese solubility and water quality under changing climatic conditions. In nature-based systems like denitrifying woodchip bioreactors (WBRs), redox-active iron and manganese minerals were shown to enhance the oxidative decomposition of woody lignocellulosic biomass, releasing bioavailable carbon that supports microbial denitrification. The interplay between dissolved oxygen exposure and mineral-driven oxidative processes significantly improved wood degradation and nitrate removal efficiency, providing a new perspective on how organo-mineral interactions impact coupled carbon and nutrient cycling in the environment. Furthermore, experiments with mineral-coated woodchips revealed contrasting effects of iron and manganese under varying redox conditions: oxic-anoxic cycling accelerated lignocellulose breakdown, while under strictly anoxic conditions minerals stabilized organic matter and slowed decomposition. In conclusion, these findings advance the understanding of Mn cycling in reservoirs and the dual roles of Mn and Fe in enhancing the efficiency of wood degradation and nitrate removal in bioreactors. They provide actionable insights for optimizing reservoir management and denitrifying bioreactor performance, addressing key environmental challenges in water quality improvement, nutrient cycling, and carbon cycling.