The presence of anthropogenic organic micropollutants in rivers poses a long-term threat to surface water quality. To describe and quantify the in-stream fate of single micropollutants, the advection–dispersion–reaction (ADR) equation has been used previously. Understanding the dynamics of the mixture effects and cytotoxicity that are cumulatively caused by micropollutant mixtures along their flow path in rivers requires a new concept. Thus, we extended the ADR equation from single micropollutants to defined mixtures and then to the measured mixture effects of micropollutants extracted from the same river water samples. Effects (single and mixture) are expressed as effect units and toxic units, the inverse of effect concentrations and inhibitory concentrations, respectively, quantified using a panel of in vitro bioassays. We performed a Lagrangian sampling campaign under unsteady flow, collecting river water that was impacted by a wastewater treatment plant (WWTP) effluent. To reduce the computational time, the solution of the ADR equation was expressed by a convolution-based reactive transport approach, which was used to simulate the dynamics of the effects. The dissipation dynamics of the individual micropollutants were reproduced by the deterministic model following first-order kinetics. The dynamics of experimental mixture effects without known compositions were captured by the model ensemble obtained through Bayesian calibration. The highly fluctuating WWTP effluent discharge dominated the temporal patterns of the effect fluxes in the river. Minor inputs likely from surface runoff and pesticide diffusion might contribute to the general effect and cytotoxicity pattern but could not be confirmed by the model-based analysis of the available effect and chemical data.