Coastal lagoons and estuaries are hot spots to accumulate river basin-related plastic leakage. However, no official methodology exists to investigate their relatively short, rich in organic matter beaches, and the knowledge of pollution of lagoons is scarce worldwide. This study aimed to develop a methodology suitable for large micro (2–5 mm), meso (5–25 mm), and macro-litter (>25 mm) monitoring at sandy inner-coastal waters that would provide comparable results to the intensively used OSPAR 100 m method. The method proposed in this study is based on two 40 m2rectangular polygons placed on the tidal accumulation zone for macro-litter enumeration and two 1 m2squares for micro- and meso-litter. This method has been applied to 23 beaches from three inner-coastal waters of the Baltic Sea. This study shows that the litter densities between lagoons and bays differ and depend on the river output intensity and the retention capacity. The “Construction material”, “Plastic pieces 2–5 mm”, and “Plastic pieces 5–25 mm” were among this study’s top ten most common litter items. Experts allocated these items to the “Land based industry and trade” source, which indicates that lagoons and bays through the connection of the major rivers could be a potential sink of land-based litter. An evident strength of the methodology established is the capability to determine litter of all sizes, low-cost and time-efficiency, implementable for volunteer-based monitoring; provides comparable results to the most commonly used methods for investigating litter pollution on coastal beaches.