Storm events lead to agricultural and urban runoff, to mobilization of contaminated particulate matter, and to input from combined sewer overflows into rivers. We conducted time-resolved sampling during a storm event at the Ammer River, southwest Germany, which is representative of small river systems in densely populated areas with a temperate climate. Suspended particulate matter (SPM) and water from 2 sampling sites were separately analyzed by a multi-analyte liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for 97 environmentally relevant organic micropollutants and with 2 in vitro bioassays. Oxidative stress response (AREc32) may become activated by various stressors covering a broad range of physicochemical properties and induction of aryl hydrocarbon receptor-chemical-activated luciferase gene expression (AhR-CALUX) by hydrophobic compounds such as dioxins and dioxin-like molecules. Compound numbers, concentrations, their mass fluxes, and associated effect fluxes increased substantially during the storm event. Micropollutants detected in water and on SPM pointed toward inputs from combined sewer overflow (e.g., caffeine, paracetamol), urban runoff (e.g., mecoprop, terbutryn), and agricultural areas (e.g., azoxystrobin, bentazone). Particle-facilitated transport of triphenylphosphate and tris(1-chloro-2-propyl) phosphate accounted for up to 34 and 33% of the total mass flux even though SPM concentrations were <1 g L-1. Effect fluxes attributed to SPM were similar or higher than in the water phase. The important role of SPM-bound transport emphasizes the need to consider not only concentrations but also mass and effect fluxes for surface water quality assessment and wastewater/stormwater treatment options.