Water quality sensors deployed on boats, buoys, and fixed monitoring stations along rivers allow high frequency monitoring at dense spatial and temporal resolutions. Research characterizing nitrate (NO3–N) delivery along extended reaches of navigable rivers, however, is sparse. Since land use and stream biogeochemistry can vary within agricultural watersheds, identifying detailed spatial patterns of stream NO3–N can help identify source area contributions that can be used to develop strategies for water quality improvement. Identifying spatial patterns is especially critical in agricultural watersheds that span multiple landscapes and have dynamic hydrological regimes. We developed and tested a new method that quantifies NO3–N delivery to streams at a high spatial resolution by continuously measuring stream NO3–N using a boat-deployed sensor. Traveling up the Iowa and Cedar Rivers (located within agricultural Upper Mississippi River Basin) and their major tributaries with the system, we automatically measured NO3–N concentrations every 15 s during four excursions spanning the months of May to August, 2018, and characterized stream NO3–N both laterally and longitudinally in river flow. Iowa River NO3–N concentrations were highest nearest the headwaters and gradually declined as the river flowed toward the Mississippi River. Conversely, Cedar River NO3–N concentrations increased from the headwaters toward the mid-watershed areas due to elevated NO3–N delivery from tributaries of the Middle Cedar River; NO3–N concentrations declined in the lower reaches. Our results confirm that NO3–N mitigation efforts should focus on level and intensely-farmed subwatersheds. Data collected with our sensor system compliments permanently deployed sensors and provides an option to support NO3–N removal efforts.