N-loads from subsurface, drains, and groundwater-fed surface (bypass) flows via two riparian zones (crop field and wetland) to a second order stream were investigated by sampling of shallow and deep groundwater on both sides and monthly measurements of flows from springs, drains, and stream including water quality (nitrate). A push-pull test in the crop field gave estimates of first-order denitrification rate (0.23 day–1). Reactive transport modelling evaluated observations of water chemistry and denitrification processes in the groundwater below the crop field showing that nitrate was completely removed by denitrification with pyrite in the aquifer (model rates of 0.6–2.5 mmol NO3 L−1 yr−1). A drain in the crop field routed approximately 10% (bypass) of the regional groundwater inflow to the stream. Buffer efficiency was high at 90%. The wetland on the other side of the stream hosts several locations of focused nitrate-rich groundwater-fed spring discharge, predominantly through a non-maintained drainage system of drainpipes and ditches with bypass accounting for 59% of the regional flow input. Nitrate was completely removed in groundwater by denitrification with dissolved organic matter in shallow groundwater. The regional inflow and N load to the wetland is amongst the highest recorded and data shows that the N load to the stream is very high. The buffer efficiency ranged from 45–83% depending on if all springs contributed to the stream or only the two with visible outflow. A conceptual model for nitrate removal efficiency as a function of Damköhler number and percent bypass flow is proposed.