Elevated nutrient inputs challenge the health and functioning of aquatic ecosystems. To improve riverine water quality management, it is necessary to understand the underlying biogeochemical and physical processes, anthropogenic drivers and their interactions at catchment scale. We hypothesize that the spatial heterogeneity of nutrient sources dominantly controls the variability of in‐stream concentration dynamics among catchments. We investigated controls of mean nitrate (NO₃^‐), phosphate (PO₄^3‐), and total organic carbon (TOC) concentrations and concentration‐discharge (C‐Q) relationships in 787 German catchments of a newly assembled data base, covering a wide range of physiographic and anthropogenic settings. We linked water quality metrics to catchment characteristics using partial least square regressions and random forests. We found archetypal C‐Q patterns with enrichment dominating NO₃^‐ and TOC, and dilution dominating PO₄^3‐ export. Both the mean NO₃^‐ concentrations and their variance among sites increased with agricultural land use. We argue that subsurface denitrification can buffer high N‐inputs and cause a decline in concentration with depth, resulting in chemodynamic, strongly positive C‐Q patterns. Mean PO₄^3‐ concentrations were related to point sources, though the low predictive power suggests effects of unaccounted in‐stream processes. In contrast, high diffuse agricultural inputs explained observed positive PO₄^3‐ C‐Q patterns. TOC levels were positively linked to the abundance of riparian wetlands, while hydrological descriptors were important for explaining TOC dynamics. Our study shows a strong modulation of anthropogenic inputs by natural controls for NO₃^‐ and PO₄^3‐ concentrations and dynamics, while for TOC only natural controls dominate observed patterns across Germany.