Delineating pollutant reactive transport pathways that connect local land use patterns to surface water is an important goal. This work illustrates high-resolution river mapping of salinity or specific conductance (SC) and nitrate ( urn:x-wiley:00431397:media:wrcr22929:wrcr22929-math-0001) as a potential part of achieving this goal. We observed longitudinal river SC and nitrate distributions using high-resolution synoptic in situ sensing along the lower Merced River (38 river km) in Central California (USA) from 2010 to 2012. We calibrated a distributed groundwater-surface water (GW-SW) discharge model for a conservative solute using 13 synoptic SC sampling events at flows ranging from 1.3 to 31.6 m3 s?1. Nitrogen loads ranged from 0.3 to 1.6 kg N d?1 and were greater following an extended high flow period during a wet winter. Applying the distributed GW-SW discharge estimates to a simplistic reactive nitrate transport model, the model reproduced observed river nitrate distribution well (RRMSE?=?5?21%), with dimensionless watershed-averaged nitrate removal (kt) ranging from 0 to 0.43. Estimates were uncertain due to GW nitrate data variability, but the resulting range was consistent with prior removal estimates. At the segment scale, estimated GW-SW nitrate loading ranged from 0 to 17 g urn:x-wiley:00431397:media:wrcr22929:wrcr22929-math-0002 s?1 km?1. Local loading peaked near the middle of the study reach, a location that coincides with a shallow clay lens and with confined animal feed operations in close proximity to the river. Overall, the results demonstrate the potential for high-resolution synoptic monitoring to support GW-SW modeling efforts aimed at understanding and managing nonpoint source pollution.