Rivers are important transport pathways for microplastics into the ocean, but they can also be potential sinks due to microplastic deposition in the sediments of the river bed and adjacent floodplains. In particular, floods can (re)mobilise microplastics from sediments and floodplains, (re)deposit and relocate them depending on the floodplain topography. The knowledge about fluvial microplastic input to floodplains, their spatial distribution and their fate in floodplain soils is limited. To investigate this topic, we sampled soil at a depth of 5–20 cm along three transects in three different Rhine floodplains. We analysed the soil samples in tandem with pyrolysis GC/MS and ATR- & μ-FPA-FTIR for their microplastic abundance and mass concentrations. To study the influence of flood frequency on the microplastic abundance in the three floodplains, we fitted a hydrodynamic flood model (MIKE 21, DHI, Hørsholm, Denmark) and related the results to the respective spatial microplastic distribution. We found similar microplastic distribution patterns in each floodplain. The highest microplastic abundance (8516–70,124 microplastics kg−1) and mass concentration (46.2–141.6 mg kg−1) were consistently found in the farthest transects from the Rhine in a topographical depression. This microplastic distribution pattern is detectable with both, pyrolysis GC/MS and FTIR. The strongest correlation between the results of both methods was found for small, abundant microplastic particles. Our results suggest that the spatial distribution of microplastics in floodplains is related to the combination of flood frequency and local topography, that ought to be explicitly considered in future studies conducted in floodplains. Finally, our results indicate that pyrolysis GC/MS and FTIR data are comparable under certain conditions, which may help in the decision for the analytical method and sampling design in future studies.