Rivers are vital water sources for humans and homes for aquatic organisms. Conversely, they are well known as the route of plastics into the ocean. Despite being the world’s number one emitter of riverine plastics into the ocean, microplastics (MPs), or plastic particles less than 5 mm, in the Philippines’ rivers are relatively unexplored. Water samples were collected from six sampling stations along the river channel of the Cagayan de Oro River, one of the largest rivers in Northern Mindanao, Philippines. The extracted microplastics’ abundance, distribution, and characteristics were analyzed using a stereomicroscope and Fourier transform infrared spectroscopy (FTIR). The results showed a mean concentration of 300 items/m3of MPs dominated by blue-colored (59%), fiber (63%), 0.3–0.5 mm (44%), and polyacetylene (48%) particles. The highest concentration of microplastics was recorded near the mouth of the river, and the lowest was in the middle area. The findings indicated a significant difference in MP concentration at the sampling stations. This study is the first assessment of microplastic in a river in Mindanao. The results of this study will aid in formulating mitigation strategies for reducing riverine plastic emissions.