The aquatic ecosystems of the world are highly burdened with microplastics (MPs; particles <5 mm). There is a great need for better understanding of patterns of MP pollution across catchments and rivers of different sizes, anthropogenic pressures and hydrogeomorphological features. In this study, we investigated the MP concentrations including their characteristics (polymer type, shape, size and colour), and MP distribution in water and sediments of two hydrogeomorphologically different small-scale catchments (< 800 km), namely Kamniška Bistrica (KB) and Ljubljanica (LJ), Slovenia. The main objective of this study was to gain a better understanding of how WWTP effluents and catchment urbanisation together with the diversity of natural hydrogeomorphology, affect the quantity and quality of MP pollutants in the rivers with smaller catchments. Significantly different mean MP concentrations were found in the water columns (KB: 59 ± 16 items m; LJ: 31 ± 14 items m), but not in the sediments (KB: 22 ± 20 items kg; LJ: 23 ± 25 items kg). A longitudinal gradient with increasing particle concentration was observed in both water and sediment samples and in both catchments. Polyethylene (PE) and polypropylene (PP) particles dominated in all samples. Fibres were predominant in the water column samples, while fragments were more common in the sediment samples. MP particles were mostly coloured, and most of them were smaller than 2 mm in both water and sediment samples. The critical evaluation of the results and previous studies suggest that the characteristics of the catchment (anthropogenic pressures, size, climate, etc.), the hydrogeomorphology of the river (sediment type, discharge, flow velocity etc.), the sampling location along the river, the sampled compartment (water, sediment), the sampling method, and the hydrometeorological characteristics at the time of sampling, are important factors for observed MP concentrations and other characteristics.