The quality of water in rivers depends on many hydrological and anthropogenic factors. The Mūša catchment belonging to the northern part of Lithuania was taken for water quality investigation. In this catchment 63% of the territory is under arable land. A conceptual FYRIS model was chosen to identify the impact of the sources of pollution with total nitrogen (N) in the Mūša river. The modelling encompasses 1997-2011 period. Having preformed calibration the model efficiency coefficient was E = 0.46, which was fairly good and correlation coefficient was r = 0.69. Having analysed total nitrogen load into the Mūša catchment from different pollution sources it was established that about 87% of it come from arable land, 10% enter from waste water treatment plants (WWTP), households and urban territories and only 3% of all nitrogen within the catchment come from wooded territories and pastures. The analysis of the results of simulation shows the seasonal amounts of scoured total nitrogen were different. Their highest amounts got to the rivers during the winter (January, February, December) season -36% of total nitrogen, when there is no vegetation processes. The highest loads 35-37% from the scattered pollution sources. In spring (March, April), in the period of snow melting, one third, i. e., 31% was scoured because of a higher runoff to the researched subcatchment. And in the summer (May, June, July, August) and autumn (September, October, November) seasons, respectively, 16 and 17% of all nitrogen falling to the subcatchment.