Microplastic pollution has become a global concern, with potential negative impacts on various ecosystems and wildlife species. Among these species, ducks (Anas platyrhynchos) are particularly vulnerable due to their feeding habits and proximity to aquatic environments contaminated with microplastics. The current study was designed to monitor microplastic (MP) pollutants in the freshwater ecosystem of the Panjkora River, Lower Dir, Pakistan. A total of twenty (20) duck samples were brought up for four months and 13 days on the banks of the river, with no food intake outside the river. When they reached an average weight of 2.41 ± 0.53 kg, all samples were sacrificed, dissected, and transported in an ice box to the laboratory for further analysis. After sample preparation, such as digestion with 10% potassium hydroxide (KOH), density separation, filtration, and identification, the MP content was counted. A total of 2033 MP particles were recovered from 20 ducks with a mean value of 44.6 ± 15.8 MPs/crop and 57.05 ± 18.7 MPs/gizzard. MPs detected in surface water were 31.2 ± 15.5 MPs/L. The major shape types of MPs recovered were fragments in crop (67%) and gizzard (58%) samples and fibers in surface water (56%). Other types of particles recovered were fibers, sheets, and foams. The majority of these detected MP particles were in the size range of 300–500 µm (63%) in crops, and 50–150 µm (55%) in gizzards, while in water samples the most detected particles were in the range of 150–300 µm (61%). Chemical characterization by FTIR found six types of polymers. Low-density polyethylene (LDPE) had the greatest polymer detection rate (39.2%), followed by polyvinyl chloride (PVC) (28.3%), high-density polyethylene (HDPE) (22.7%), polystyrene (6.6%), co-polymerized polypropylene (2.5%), and polypropylene homopolymer (0.7%). This study investigated the presence of microplastics in the crops and gizzards of ducks, as well as in river surface water. The results revealed the significant and pervasive occurrence of microplastics in both the avian digestive systems and the surrounding water environment. These findings highlight the potential threat of microplastic pollution to wildlife and ecosystems, emphasizing the need for further research and effective mitigation strategies to address this pressing environmental concern.