The statistical model MESAW (Matrix Equations for Source Apportionment on Watershed) was used to estimate the diffuse unit-area source emission coefficients of nitrogen in Estonian rivers. The input data included monitored riverine loads, point sources and land use categories from a total of 50 rivers/catchment areas. Two independent studies were conducted: the estimation of emission coefficients for the whole of Estonia and for a smaller study area near Tallinn. The results from both cases showed that drained peat soils were the highest diffuse source contributor in unit-area loads. The results show that the unit-area loads from drained peat soils were up to 2.3 times higher than from arable land. Moreover, a comparison of emission coefficients for the whole of Estonia and for the Tallinn catchment area indicated that coefficients can vary significantly between sources and single years. Additional detailed studies and monitoring are needed to support these conclusions.