Background: Estuaries are highly productive ecosystems characterised by constant environmental variability, which makes frequent monitorization essential. Estuaries are among some of the most impacted ecosystems, often surrounded by densely urbanised areas and exposed to multiple pollution sources. Microplastics (MPs) are an emerging pollutant that harm aquatic organisms and potentially pose risks to human health. However, MP are still not included in current European water quality guidelines. In this context, the present study assessed the ecological quality of the Douro estuary, in accordance with the Water Framework Directive (WFD), and evaluated the distribution of MPs within this ecosystem. Methods: The ecological evaluation consisted of the analysis of physical and chemical parameters, phytoplankton biomass, macroinvertebrate community, sediment’s organic matter, and granulometry. Along the low estuary, 12 sites were assessed, and MPs were sampled in four transects. Water samples were collected from the surface and sub-surface areas. In sediment, MPs were also sampled along with ecological parameters. MPs were counted, and classified according to size, typology and colour. Results: Physical and chemical results revealed a moderate ecological status, driven by NO₂+NO₃ concentrations above reference values (1 mg N/L). Phytoplankton biomass showed a high ecological status across all sites. Regarding the macroinvertebrate community, the estuary was classified with a Moderate ecological status. Sediments exhibited low organic matter and a mixed granulometric profile. A total of 9.03 MP m^-3 in water and 1650 MP Kg^-1 in sediments were recorded, values above those described in Portuguese rivers. A Principal Coordinates Analysis with MP characteristics revealed differences among transects and samples areas consistent with a higher hydrodynamic effect. Conclusion: The estuary holds a Moderate ecological status according to the WFD. MP contamination was also identified across the estuary, although further work is required to identify specific pollution sources.