Abstract. The objective of this study was the detection and assessment of nutrient entry pathways in a complex mesoscale lowland catchment. The central aim was the development of a transferable method for an efficient estimation of instream water quality in rural environments. The investigated Kielstau catchment with a size of approximately 50 km 2 is located in the North German lowlands. Land use is dominated by agriculture as well as pasture and is characterised by extensive artificial drainage systems. Additionally wastewater treatment plants influence the river water quality.Six measuring campaigns were carried out over the period of one year. Each time, water quality was assessed at 16 locations along a 12 km longitudinal transect of the stream to consider the influence of each tributary or inflow. The results showed that the applied measuring method was useful to assess nutrient entry pathways into surface waters from diffuse and point sources. Some tributaries increased the main stream NO 3 -N concentrations especially in autumn. Using a German classification system (LAWA, 1998), the NO 3 -N results can mostly be assigned to water quality class III (heavily contaminated). Water balance and nitrate loads were modelled with the river basin scale model SWAT (Soil and Water Assessment Tool, Arnold et al., 1998). The measured and modelled discharges showed a good correlation. While nitrate load range and dynamics are well represented during the summer periods, they show a poor correlation during the winter period.