Results: All sites of both rivers under higher pressure did not reach a “good” ecological status (S2–S3, C2–C4) based on the macroinvertebrate community.

High levels of nutrients were observed at all sites in both rivers (except C2), especially phosphorus. In the Oligochaeta’s gut of Costa-Couros river, the high number of MPs seems to be associated with their weight (95.25 ± 25.61 to 1069.00 ± 385.30 MPs g/fresh weight), suggesting the existence of malnutrition and digestive disorders, whereas the highest number of MPs in gut (134.00 ± 30.36 to 558.6 ± 100.70 MPs g/fresh weight) were found for the heaviest organisms of Selho. Conclusions: Thus, sites with higher ecological status do not necessarily have lower abundance of MPs. In the sediments, urbanization seems to be the main driver for MP contamination. MP contamination is pervasive across the sediments and Oligochaeta’s gut in both rivers. Since MPs have the potential to cause harm to environmental and human health, it is essential to monitor not only the ecological status of freshwaters, but also emerging pollutants such as MPs.