River water can be used to recharge aquifers exploited for drinking water production. Several recent studies reported microplastics (MPs) in river water, and therefore, the potential contamination of groundwater by MPs is a growing concern among stakeholders and citizens. In this research, we investigate the fate of MPs (> 20 μm) along six different stages of a major Managed Aquifer Recharge (MAR)-water supply system in Switzerland. About 20 l of water were filtered using steel meshes at each location in triplicates. In the laboratory, MPs deposited on the anodisc filters were identified using Focal Plane Array (FPA) micro-Fourier-Transform-InfraRed (μFTIR) spectroscopy. The obtained hyperspectral data were processed using the imaging software Microplastics Finder for MPs identification and classification. Our results revealed a 20-fold decrease in MPs concentration from the Rhine River bed water (112 ± 27.4 MPs/l) to after the coagulation, flocculation and sedimentation (5.5 ± 2.2 MPs/l), a further 3-fold decrease to after the sand-filtration system (1.8 ± 0.9 MPs/l), corresponding to an overall removal efficiency of 98.4 %. The MPs concentrations remained low following MAR (2.7 ± 0.7 MPs/l) through a Quaternary gravel aquifer. Activated carbon filters did not substantially further reduce MPs concentrations. The percentage of fragments (≈95 %) prevailed over fibers (≈5 %) at all locations, with fibers being longer and more abundant in the river water. Overall, this study demonstrates the effectiveness of the treatment systems to remove MPs larger than 20 μm. Finally, we calculated an uncertainty in MPs concentrations of one order of magnitude depending on the user-defined parameters inside the MPs identification and classification model. The Quality Assurance/Quality Control approach followed during laboratory analysis highlighted an accumulation of surrogate particles at the edges of the disc, which would have an impact for MPs number upscaling.