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The supply of terrestrial dissolved organic carbon (DOC) to aquatic ecosystems affects local in-stream processes and downstream transport of DOC in the fluvial network. However, we have an incomplete understanding on how terrestrial DOC inputs alter longitudinal variations of DOC concentration along headwater stream reaches because groundwater discharge, groundwater DOC concentration and in-stream DOC uptake vary at relatively short spatial and temporal scales. In the riparian zone, the convergence of subsurface flow paths can facilitate the inflow of terrestrial DOC from large upslope contributing areas to narrow sections of the stream. We refer to these areas of flow path convergence as discrete riparian inflow points (DRIPs). In this study, we ask how longitudinal patterns of stream DOC concentrations are affected by DRIPs, as they are major inputs of terrestrial DOC and important locations for in-stream processes. We used a mixing model to simulate stream DOC concentrations along a 1.5 km headwater reach for fifteen sampling campaigns with flow conditions ranging from droughts to floods. Four sets of model scenarios were used to compare different representations of hydrology (distributed inputs of DRIPs vs diffuse groundwater inflow), and in-stream processes (passive transport vs in-stream biological uptake). Results showed that under medium (10–50 l/s) and high flow conditions (> 50 l/s), accounting for lateral groundwater inputs from DRIPs improved simulations of stream DOC concentrations along the reach. Moreover, in-stream biological uptake improved simulations across low to medium flow conditions (