System dynamics modeling was performed in Brubäcken, the mine water recipient at Boliden, with the aim of predicting nitrogen transformations in the system. The 12-km-long Brubäcken system flows through Gillervattnet tailings impoundment and two lakes (Nya Sjön and Bruträsket), and finally discharges into the Skellefte River. Ammonium is the dominating nitrogen species in the system, and modeling focused on Nya Sjön, where NH4-N was present in concentrations up to 14 mg/l in 2006, and reached 6 mg/l in 2008. This concentration drop was related to the closing of the cyanide gold ore leach plant at Boliden in early 2008. Simulations of nitrogen transformations are based on a conceptual model that includes six nitrogen species involved in 16 different nitrogen transformation reactions occurring in the water column as well as in water- sediment and water-atmosphere interactions. Nitrogen species concentrations and process rates are simulated using the Powersim modeling software. Most of the reactions are considered to follow first-order kinetics Simulations showed high correlation between measured and predicted concentrations. The long-term stability of the model was tested in a six- year simulation using similar input data for all years. The stability of the model is judged to be satisfactory. A sensitivity analysis was also performed to identify the behavior of the model when input variables change ±10%. The results are presented graphically, and the most influential variables are identified. The model was finally validated using data from two years (2006–2007).