<p>This study provides a comprehensive picture of the distribution and abundance of microplastics (MPs) in the water, sediment, and animals of the Nile River in Upper Egypt. MPs were found in all collected samples from all sites with significant differences in their abundance and distribution. Edfu had the highest MPs abundances in both water and sediment. For fauna, crayfish were the most abundant MPs in the gills, and African catfish had the most abundant MPs in the alimentary canal, and they were the only species that had a significant difference in MPs distributed in their alimentary canal and gills. For Nile tilapia and African catfish from Nagaa Hammadi site had the highest MPs abundance in their alimentary canals. El-wasta also had the highest MPs abundance in the gills for both Nile tilapia and African catfish, and in alimentary canal and gills of crayfish. These findings can be used to direct future investigations into how MPs interact with the Nile ecosystem, which will aid officials in determining the most effective way to eliminate this pollutant.</p>