The ubiquitous nature of microplastics in the marine environment has been reported globally for both sediment and surface waters. However, few studies have reported on the present status of microplastics pollution in coastal areas of Japan. The inconsistency in sampling techniques, methods of extraction, and units of reporting microplastic concentrations prove to be a major challenge in this emerging field, especially for microplastics in marine sediments, highlighting the need for reproducible methods and data to assess the extent of microplastic pollution in the marine environment, understand their dynamics and design management strategies to tackle this environmental problem. This study encompasses a large geographic range with diverse socio-economic context and provides baseline data on microplastics in coastal waters and sediment around Japan. The data obtained showed higher concentrations of microplastics in sediments than in surface water suggesting a high rate of sedimentation occurring in coastal areas, especially for the larger-sized and denser plastic particles. Thus, sediment may represent an important sink for microplastics in coastal areas.