The rapid source identification and environmental risk assessment (ERA) of hundreds of chemicals of emerging concern (CECs) in river water represent a significant analytical challenge. Herein, a potential solution involving a rapid direct-injection liquid chromatography-tandem mass spectrometry method for the quantitative determination of 102 CECs (151 qualitatively) in river water is presented and applied across six rivers in Germany and Switzerland at high spatial resolution. The method required an injection volume of only 10 µL of filtered sample, with a runtime of 5.5 min including re-equilibration with >10 datapoints per peak per transition (mostly 2 per compound), and 36 stable isotope-labelled standards. Performance was excellent from the low ng/L to µg/L concentration level, with 260 injections possible in any 24 h period. The method was applied in three separate campaigns focusing on the ERA of rivers impacted by wastewater effluent discharges (1 urban area in the Basel city region with 4 rivers, as well as 1 semi-rural and 1 rural area, each focusing on 1 river). Between 25 and 40 compounds were quantified directly in each campaign, and in all cases small tributary rivers showed higher CEC concentrations (e.g., up to ~4000 ng/L in total in the R. Schwarzach, Bavaria, Germany). The source of selected CECs could also be identified and differentiated from other sources at pre- and post- wastewater treatment plant effluent discharge points, as well as the effect of dilution downstream, which occurred over very short distances in all cases. Lastly, ERA for 41 CECs was performed at specific impacted sites, with risk quotients (RQs) at 1 or more sites estimated as high risk (RQ > 10) for 1 pharmaceutical (diclofenac), medium risk (RQ of 1-10) for 3 CECs (carbamazepine, venlafaxine, and sulfamethoxazole), and low risk (RQ = 0.1-1.0) for 7 CECs (i.e., RQ > 0.1 for 11 CECs in total). The application of high-throughput methods like this could enable a better understanding of the risks of CECs, especially in low flow/volume tributary rivers at scale and with high resolution.