Excessive amounts of nutrients and dissolved organic matter in freshwater bodies affect aquatic ecosystems. In this study, the spatial and temporal variability in nitrate (NO^-₃), dissolved organic carbon (DOC) and soluble reactive phosphorus (SRP) was analyzed in the Selke (Germany) river continuum from three headwaters draining 1-3 km² catchments to two downstream reaches representing spatially integrated signals from 184-456 km² catchments. Three headwater catchments were selected as archetypes of the main landscape units (land use × lithology) present in the Selke catchment. Export regimes in headwater catchments were interpreted in terms of NO^-₃, DOC and SRP land-to-stream transfer processes. Headwater signals were subtracted from downstream signals, with the differences interpreted in terms of in-stream processes and contributions from point sources. The seasonal dynamics for NO^-₃ were opposite those of DOC and SRP in all three headwater catchments, and spatial differences also showed NO^-₃ contrasting with DOC and SRP. These dynamics were interpreted as the result of the interplay of hydrological and biogeochemical processes, for which riparian zones were hypothesized to play a determining role. In the two downstream reaches, NO^-₃ was transported almost conservatively, whereas DOC was consumed and produced in the upper and lower river sections, respectively. The natural export regime of SRP in the three headwater catchments mimicked a point-source signal (high SRP during summer low flow), which may lead to overestimation of domestic contributions in the downstream reaches. Monitoring the river continuum from headwaters to downstream reaches proved effective to jointly investigate land-to-stream and instream transport, and transformation processes.