Dissolved O2 (DO) concentration is critical to determining ecosystem functions such as organic matter respiration, which can favor fixed nitrogen loss and the accumulation of compounds such as NH4+. This dynamic is observed in central Chile's coastal upwelling system (36 °S), which presents seasonally O2 deficient waters and high biological productivity. Temporal dynamics for dissolved inorganic nitrogen (DIN: NO3−, NO2− and NH4+) are analyzed based on a ten year time series of monthly measurements of DO and DIN and a three year record of absolute DIN uptake rates (ρDIN), respective turnover rates (νDIN), and O2 utilization rates (OUR). Observed O2 deficit gradually increases from hypoxia to near anoxia as the system becomes more productive, favoring the accumulation of NO2− and NH4+. Three temporal phases within the aphotic layer were distinguished: (I) DO > 62 μmol L−1 (May to August), (II) 5 < DO < 62 μmol L−1 (September to December) and (III) DO < 5 μmol L−1 (January to April). From phase I to III, DO and NO3− inventories decreased by eight and two times, respectively, while NH4+ and NO2 inventories increased two- and five-fold, respectively. Uptake rates for NH4+ varied from 0.23 to 450 nmol N L−1 d−1 and from 1.42 to 184 nmol N L−1 d−1 for NO3−. Notably, integrated ρNH4+ increased during phase III, generating a NH4+ turnover time of 12–29 days; whereas integrated ρNO3− peaked during phase II, and removed the NO3− pool over an extended turnover time (>820 days). Integrated OUR gradually increased from phase I to III (from 225 to 422 mmol m−2 d−1), with DO pools replenished over 2.3 to 26 days. NH4+ regeneration rates ranged from 34 to 62 mmol m−2 d−1 and NH4+ pools were replenished within a few days. Variation in DO, which regulates N cycling, may explain the accumulation of N-species within the aphotic layer. Observed trends could be extrapolated to scenarios of upwelling-favorable winds, eutrophication and hypoxia.