The Black Rock Desert Basin is not a unified drainage basin. Rather it is a collection of closed basins, largely disconnected from one another and grouped together by the USGS in their hierarchical hydrologic unit system. At the smallest, 12-digit HUC subwatershed level, there are 19 separate closed basins within the Black Rock Desert Basin. One of these is the Black Rock Desert Subwatershed (HUC 160402021600). Others have names like Calcutta Lake, Mosquito Lake, Long Valley, Town of Empire, Rock Creek-Hualapai Flat, and so on.<ref name=WBD/>
The Smoke Creek (southwest) and Massacre Lake (northwest) subbasins extend into California, while the Upper Quinn (east) and Thousand-Virgin (north-central) subbasins extend into Oregon.<ref name=USGS/> The subbasins are primarily in the Northern Basin and Range ecoregion, but the lengthy southeast edge extends into the Central Basin and Range ecoregion.
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