Microplastics in freshwater ecosystems have gained attention for their potential impact on biodiversity. Rivers are complex and dynamic ecosystems that transport particles and organic matter from the headwaters through watersheds to the ocean. Changes in land use and the presence of wastewater treatment plants (WWTPs) increase the risk of plastic contamination. Simultaneously, hydromorphological features of the watershed can influence the dispersion and retention of microplastics. This study assesses the impact of urban land uses and river hydromorphology on microplastic abundance and spatial distribution in two watersheds with contrasting land uses. Unexpectedly, our findings show that microplastics were widespread throughout watersheds both in water (3.5 ± 3.3 particles/L) and sediments (56.9 ± 39.9 particles/g). The concentration of microplastics in sediments significantly increased in granulometry ranging from 0.5 to 1 mm. Microplastics in running waters are significantly correlated with increasing urban land use coverage. However, the presence and distance of WWTPs did not affect microplastic distribution. In conclusion, contrasting patterns were observed for suspended and sedimented microplastic particles: suspended microplastics were associated with an anthropogenic effect, whereas the concentration of microplastics in sediments was determined by riverbed granulometry. Our results suggest that the interaction of anthropogenic and environmental factors shapes microplastic distribution along the rivers and their subsequent transport toward the coastal ocean. Finally, a review of the current literature reveals the absence of standardization in field and laboratory assessment techniques and measurement units, representing a challenge for intercomparisons of river microplastic studies.