Microplastics (MPs) are an emerging pollutant of concern in all known aquatic ecosystems. However, studies at a regional scale on MP pollution in freshwater systems and the necessary risk assessments are limited. Therefore, in this study, we examined microplastic concentrations, size distributions, and polymer types in surface waters and sediments in the geographic region Flanders (Belgium), as a case study for a densely populated region and one of the most developed parts of Europe. Samples have been taken on nine different locations, of which five were repeated in a different weather condition. In total 43 aqueous and nine sediment samples have been collected. The quantity and identity of the microplastics in the samples were determined with μFTIR spectroscopy in the range of 25–1000 μm. The MPs' abundances in surface waters and sediments ranged from 0 to 4.8 MP L−1 (average = 0.48 MP L−1) and from 0 to 9558 MP kg−1 dry weight (average = 2774.57 ± 2317.93 MP kg−1 DW), respectively. Polystyrene and polypropylene were the most common polymer compositions found. No correlations were observed between microplastic concentrations in the sediment/the surface water samples and the measured environmental variables rainfall, conductivity, pH, dissolved oxygen content, waterway flow rate and width, and surrounding land use. Risk assessment results for the measured surface water concentrations through the risk quotient (RQ) method and the probabilistic risk assessment framework suggest that most of the sampled sites in Flanders posed negligible risks to freshwater biota, while this was not the case for some of the sediment concentrations. Our results illustrate the need to urgently develop analytical methods that can routinely measure the full size range of MP in environmental samples to adequately assess risks for the environment.