Microplastics (MPs) are ubiquitous contaminants of emerging concern that require additional study in freshwater streams. We examined the spatial-temporal variations in MP concentrations and characteristics within two headwater basins in the Southern Appalachian Mountains of western North Carolina over ~1 year. Atmospheric samples were also collected to determine the significance of atmospheric MP deposition to these relatively small streams. MP concentrations in both basins were within the upper quartile of those reported globally, reaching maximum values of 65.1 MPs/L. Approximately 90% of MPs were fibers. MP composition was dominated by polystyrene, polyamides, and polyethylene terephthalate. Spatially, concentrations were highly variable and increased with development, indicating anthropogenic inputs from urbanized areas. MP concentrations were also elevated in forested tributary subbasins with limited anthropogenic activity, suggesting atmospheric deposition was an important MPs source. Significant atmospheric inputs are supported by high atmospheric depositional rates (ranging between 7.6 and 449.8 MPs/m2/day across our study sites) and similarities in morphology, color, and composition between atmospheric and water samples. Temporally, MP concentrations during storm events increased, decreased, or remained the same in comparison to base flows, depending on the site. The observed spatial and temporal variations in concentrations appear to be related to the complex interplay between precipitation and runoff intensities, channel transport characteristics, and MP source locations and contributions.