The global atmospheric transport of microplastics (MPs) plays a crucial role in the contamination of remote, especially higher-elevation, environments. Precipitation is considered the main source of MP pollution. Meanwhile, plastic waste generated from, for example, tourism activities can be a local source of MP pollution. In this study, we specify which of the mentioned sources of MP, global or local, have a higher impact on the pollution level in the high-elevation oligotrophic lakes of Tatra National Park in Poland. Due to its unique natural value, it is listed by UNESCO as an international biosphere reserve and meets the criteria for Natura 2000 areas. We comprehensively analyzed the morphometric and anthropogenic features of 11 lakes in terms of the contamination level, color, shape, and polymer type of the MPs found in the surface waters. MP fibers were found to be present in all studied lakes, with contamination ranging from 25 to 179 items/m³. Polypropylene, polyethylene terephthalate, and natural or semi-natural cellulose fibers—black or red in color with a length of 0.2–1.0 mm—predominated, which corresponds with other studies conducted on remote mountain ecosystems. We did not find any correlation of the number of MPs with local anthropogenic pressure characteristics. In turn, the significant correlation with lake area, coastline length, lake volume, and catchment area indicated airborne sources, including global transport of MPs to the lakes with reduced water outflow.