Emitted to the atmosphere through fire and fossil fuel combustion, refractory black carbon nanoparticles (rBC) impact human health, climate, and the carbon cycle. Eventually these particles enter aquatic environments, where they may affect the fate of other pollutants. While ubiquitous, the particles are still poorly characterized in freshwater systems. Here we present the results of a study determining rBC in waters of the Lake Tahoe watershed in the western United States from 2007 to 2009. The study period spanned a large fire within the Tahoe basin, seasonal snowmelt, and a number of storm events, which resulted in pulses of urban runoff into the lake with rBC concentrations up to 4 orders of magnitude higher than midlake concentrations. The results show that rBC pulses from both the fire and urban runoff were rapidly attenuated suggesting unexpected aggregation or degradation of the particles. We find that those processes prevent rBC concentrations from building up in the clear and oligotrophic Lake Tahoe. This rapid removal of rBC soon after entry into the lake has implications for the transport of rBC in the global aquatic environment and the flux of rBC from continents to the global ocean.