Microplastics (MP) have been reported in many rivers across the globe but their depositional and archiving mechanisms in sediments are not fully understood yet. The aim of this study was to identify potential controlling factors of MP spatial distribution in surface sediment after a characterisation (sediment composition, hydrological conditions, sedimentary environment) of 14 sampling sites in an 8 km2 segment of the Loire river. Samples were collected from 3 sedimentary environments (sandbars, riverbanks and semi-active channels) with diverse flooding frequencies, grain size distributions and total organic carbon (TOC) contents. After treatment of sediment samples, MP concentrations and sizes were determined and polymer types identified by μFTIR (micro Fourier transform infrared) spectroscopy. After checking the influence of sample-scaled variability over river segment-scaled variability, MP concentrations were evaluated to 867–10635 MP/kg of sediment dry weight (sed dw, size range 25–5000 μm) in the river segment. No environmental parameters were individually correlated with MP contamination in our study, possibly due to complex depositional environments in this river segment. A systemic approach however allowed to exhibit that sediment composition reflecting hydro-morpho-sedimentary conditions can help to understand MP distribution in a river segment. A higher MP contamination observed in semi-active channel samples (median contamination value of 4797 MP/kg sed dw) could indicate that MP deposition is favoured in fine-grained (FGS) and TOC-rich sediment, reflecting less energetic hydrological conditions. Moreover, increasing flooding frequency seems to favor accumulation of MP only in the case of semi-active channels. On the contrary, less MP were detected in sandbars and riverbanks (median contamination of 1296 MP/kg sed dw), formed in higher hydrodynamical energy conditions. As a 10-fold variability of MP concentration exists in the study area, the importance of multiplying replicates even at the scale of a small river segment is underlined to access representativity of MP contamination.