Concentrations of inorganic nitrogen (N) in non-polluted and undisturbed northern rivers are often lower during summer than during the dormant season. The great difference between summer and winter N concentrations probably reflects higher soil water N contents in the dormant season compared with the growing season, when inorganic N is usually retained effectively. Microbial activity in soil is observed even in sub-zero temperatures and it is generally assumed that in the northern latitudes some N mineralization occurs during winter. The dynamic, semi-distributed INCA (Integrated Nitrogen in Catchments) model was applied to the Simojoki river basin in the boreal zone in northern Finland. With this model process rates and loads of N can be simulated in different land use modes. The INCA model was not able to simulate the high inorganic N concentrations in the river water in winter unless N processes in sub-zero temperatures were included. The aim of this study was to compare the simulated N mineralization in two different land use modes: boreal forests on mineral soil and agricultural fields. Net N mineralization occurring during the season when soil is mainly frozen (November–April) accounted for 43% of the annual N mineralization. This work indicates the importance of over-winter N processes in northern areas, which should be taken into account when modelling nutrient leaching.