Abstract. Rivers may act as important sinks (filters) or sources for inorganic nutrients between the land and the sea, depending on the biogeochemical processes and nutrient inputs along the river. This study examines the inter-annual variability of dissolved inorganic nitrogen (DIN) seasonal (wet–dry) cycle for the Biobío River, one of the largest and most industrialized rivers of Central Chile (36°45'–38°49' S and 71°00'–73°20' W). Long-term water flow (1990–2012) and water quality datasets (2004–2012) were used along with a one-dimensional reactive transport ecosystem model to evaluate the effects of water flow and N inputs on seasonal pattern of DIN. From 2004 to 2012, annual average nitrate levels significantly increased from 1.73 ± 2.17 μmol L⁻¹ (upstream of the river) to 18.4 ± 12.7 μmol L⁻¹ (in the river mouth); while the annual average oxygen concentration decreased from 348 ± 22 to 278 ± 42 μmol L⁻¹ between upstream and downstream, indicating an additional oxygen consumption. Variability in the mid-section of the river (station BB8) was identified as a major influence on the inter-annual variability and appeared to be the site of a major anthropogenic disturbance. However, there was also an influence of climate on riverine DIN concentrations; high DIN production occurred during wet years, whereas high consumption proceeded during dry years. Extremely reduced river flow and drought during summer also strongly affected the annual DIN concentration, reducing the DIN production. Additionally, summer storm events during drought periods appeared to cause significant runoff resulting in nitrate inputs to the river. The total DIN input reaching the river mouth was 0.159 Gmol yr⁻¹, implying that internal production exceeds consumption processes, and identifying nitrification as one of the predominant processes occurring in the estuary. In the following, the impact on the river of DIN increases as a nutrient source, as well as climate and biogeochemical factors are discussed.