I just bought an 1870 home, and man did the basement stink!!!!
I got a dehumidifier. Humidity was 80% when I first turned it on. Now it is down to 45%, and smell is all but gone.
As far as the water....I had that too. It was because water was sitting next to foundation and seeping through the stone foundation. I installed downspout extentions to get the water farther away from house. That fixed that problem. Next year I'll build up the dirt around the house, but this works for now.