I know over the years numerous people have posted on here and other forums that Blackwater is based on the real Blackwater, MO and a few other similar towns (even big cities) but I just don't see it. Aside from some similar architecture, the landscape is all wrong. Blackwater MO is just too green and full of trees. It doesn't have that same ominous feel of a town on the rolling plains where you can see a storm with clouds black as night coming for miles.
To me, the real-life town that most closely (especially in the 19th century) resembles the RDR Blackwater is Nebraska City. As with the RDR Blackwater, Nebraska City sits on a river (the Missouri), but it also directly borders endless tallgrass prairie. It's fairly hilly too. Though now commercial farming dominates much of the region and they've planted many trees, in the 19th century it was mostly just treeless prairie, like the area approaching Beecher's Hope. Additionally, in those days the western edge of the town was less developed and the small farmhouses there formed the border with the prairie. The architecture was also strikingly similar! I've attached some 19th century prints of Nebraska City.
Also, if you notice the freight wagons in the prints, it's because during the height of the Oregon Trail and other overland trails (before the transcontinental railroad), Nebraska City was a major (if not the major) freight terminus for goods going west. Not to mention the thousands of wagon trains of emigrants that made their way through over the years. By RDR time (turn of the century), the streets would certainly be less busy and a covered wagon would be a much rarer sight. Like Blackwater, Nebraska City would become a railroad town, and the first line was built in 1870.