Although I could not find a historical reference for this, it’s most likely that Blackwater takes its name from the Blackwater Creek that runs through it and then Southwest into Hancock County, Tennessee. You can see a map of it here: http://www.placekeeper.com/Virginia/Map/Blackwater_Creek-1463534.html. This very creek runs through my parents’ property.
Any time that a river or stream contained tannins from trees and soil that make it dark, it is referred to as “blackwater”. So, this is the likely reason for the name. It’s also interesting to note that there is a Blackwater River in Southeast Virginia and a Blackwater Creek in Lynchburg, Virginia. There is also a Blackwater River in Ireland. It’s also possible that the name was brought here by the Scots-Irish settlers.
When my Uncle Paul Baker bought land in Milton, Florida, and convinced his parents to move there, they named the canal that went through the area the Blackwater Canal. They also named their road Blackwater Drive. These names were in honor of their former home place. Ironically, there is also a Blackwater River that runs near there.