The surrounding landscape of a stream has crucial impacts on the aquatic environment. This study pictures the hydro-biogeochemical situation of the Tyrebækken creek catchment in central Jutland, Denmark. The intensively managed agricultural landscape is dominated by rotational croplands. The small catchment mainly consist of sandy soil types besides organic soils along the streams. The aim of the study was to characterise the relative influence of soil type and land use on stream water quality. Nine snapshot sampling campaigns were undertaken during the growing season of 2009. Total dissolved nitrogen (TDN), nitrate (NO3−), ammonium nitrogen and dissolved organic carbon (DOC) concentrations were measured, and dissolved organic nitrogen (DON) was calculated for each grabbed sample. Electrical conductivity, pH and flow velocity were measured during sampling. Statistical analyses showed significant differences between the northern, southern and converged stream parts, especially for NO3− concentrations with average values between 1.4 mg N l−1 and 9.6 mg N l−1. Furthermore, throughout the sampling period DON concentrations increased to 2.8 mg N l−1 in the northern stream contributing up to 81% to TDN. Multiple-linear regression analyses performed between chemical data and landscape characteristics showed a significant negative influence of organic soils on instream N concentrations and corresponding losses in spite of their overall minor share of the agricultural land (12.9%). On the other hand, organic soil frequency was positively correlated to the corresponding DOC concentrations. Croplands also had a significant influence but with weaker correlations. For our case study we conclude that the fractions of coarse textured and organic soils have a major influence on N and DOC export in this intensively used landscape. Meanwhile, the contribution of DON to the total N losses was substantial.