Elevated nutrient inputs and reduced riverine concentration variability 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 and their interactions at catchment scale. We hypothesize that spatial heterogeneity of nutrient sources dominantly controls the variability of instream concentrations among different catchments. Therefore, we investigated controls of mean nitrate (NO), phosphate (PO), and total organic carbon (TOC) concentrations and concentration-discharge (C-Q) relationships from observations in 787 German catchments covering a wide range of physiographic and anthropogenic settings. Using partial least square regressions and random forests we linked water quality metrics to catchment characteristics. We found archetypal C-Q patterns with enrichment dominating NO and TOC, and dilution dominating PO export. Across the catchments, we found a positive but heteroscedastic relation between mean NO concentrations and agricultural land use. We argue that denitrification, particularly pronounced in sedimentary aquifers, buffers high inputs and causes a decline in concentration with depth resulting in chemodynamic, strongly positive C-Q patterns. Consequently, chemodynamic NO enrichment patterns could indicate effective subsurface denitrification. Mean PO concentrations were related to point sources though the low predictive power suggests effects of unaccounted processes. In contrast, diffuse inputs better explained the spatial differences in PO C-Q patterns. TOC levels were positively linked to the abundance of riparian wetlands as well as negatively to NO concentrations suggesting interacting processes. This study shows that vertical concentration heterogeneity mainly drives nutrient export dynamics, partially modified by interactions with other controls.