This study presents the most extensive investigation of microplastic (MP) contents in sediment from the Elbe River. We employed electrostatic separation (ES) and differential scanning calorimetry (DSC) to overcome limitations of sample throughput and time-consuming analysis. In total 43 sediment samples were collected using a Van-Veen grab. Subsequently, coarse materials (d₁₀ > 100 μm) and fine materials (d₁₀ ≤ 100 μm) were enriched using ES and density separation. DSC was utilized for MP identification and quantification, based on the phase-transition signals of eight different polymers. MP presence was detected in 25 samples, with successful quantification in 12 samples. The MP content in coarse material samples from shoreline areas ranged from 0.52 to 1.30 mg/kg, while in fine material samples from harbor basins, it ranged from 5.0 to 44.6 mg/kg. The most prevalent polymers identified were LD-PE, HD-PE, PP, and PCL. These findings confirmed the suitability of DSC for analyzing MP in complex environmental samples. MP hotspots were identified in harbor basins, where natural sedimentation processes and increased anthropogenic activities contribute to MP accumulation. Additionally, industrial sewage potentially contributed to MP content in sediment samples. The highest pollution levels were observed in the middle Elbe, between the confluences of Mulde and Havel. Lowest MP contents were found in the lower Elbe, potentially influenced by tides. Future studies should focus on holistic investigations of selected river sections, encompassing sediment, water, and biota samples, rather than the entire catchment area. This approach would facilitate the generation of spatiotemporal data on MP distribution in freshwater streams. In addition, more research is needed to explore potential interactions between different MP and sediment types during DSC measurements.