To understand the nitrogen (N) cycle in sediments with deep oxygen penetration, we measured pore-water profiles to calculate N fluxes and rates at 13 locations in Lake Superior in water depths ranging from 26 to 318 m. Sediments with high oxygen demand, such as in nearshore or high-sedimentation areas, contribute disproportionally to benthic N removal, despite covering only a small portion of the lake floor. These sediments are nitrate sinks (average 0.16 mmol m-2 d-1) and have denitrification rates (average 0.76 mmol m-2 d-1) that are comparable to those in coastal marine sediments. The deeply oxygenated (4 to > 12 cm) offshore sediments are nitrate sources (average 0.26 mmol m-2 d-1) and generate N2 at lower rates (average 0.10 mmol m-2 d-1). Ammonium is nitrified with high efficiency (90%), and nitrification supports > 50% of denitrification nearshore and ~ 100% offshore. Oxygen consumption by nitrification accounts for 12% of the total sediment oxygen uptake. About 2% of nitrate reduction is coupled to oxidation of iron, a rarely detected pathway. Our Lake Superior N budget indicates significant contributions from sediment-water exchanges and N2 production and is closer to balance than previous budgets. Our results reveal that sediment N cycling in large freshwater lakes is similar to that in marine systems. They further suggest that denitrification rates in slowly accumulating, well-oxygenated sediments cannot be described by the same relationship with total oxygen uptake as in high-sedimentation areas; hence, global models should treat abyssal ocean sediments differently than coastal and shelf sediments.