Anaerobic biodegradation of organic amendments and contaminants in aquifers can trigger secondary water quality impacts that impair groundwater resources. Reactive transport models help elucidate how diverse geochemical reactions control the spatiotemporal evolution of these impacts. Using extensive monitoring data from a crude oil spill site near Bemidji, Minnesota (USA), we implemented a comprehensive model that simulates secondary plumes of depleted dissolved O2 and elevated concentrations of Mn²⁺, Fe²⁺, CH₄, and Ca²⁺ over a two-dimensional cross section for 30 years following the spill. The model produces observed changes by representing multiple oil constituents and coupled carbonate and hydroxide chemistry. The model includes reactions with carbonates and Fe and Mn mineral phases, outgassing of CH₄ and CO₂ gas phases, and sorption of Fe, Mn, and H⁺. Model results demonstrate that most of the carbon loss from the oil (70%) occurs through direct outgassing from the oil source zone, greatly limiting the amount of CH₄ cycled down-gradient. The vast majority of reduced Fe is strongly attenuated on sediments, with most (91%) in the sorbed form in the model. Ferrous carbonates constitute a small fraction of the reduced Fe in simulations, but may be important for furthering the reduction of ferric oxides. The combined effect of concomitant redox reactions, sorption, and dissolved CO₂ inputs from source-zone degradation successfully reproduced observed pH. The model demonstrates that secondary water quality impacts may depend strongly on organic carbon properties, and impacts may decrease due to sorption and direct outgassing from the source zone.