The disclosure is directed generally a biomass conditioning system and methods for conditioning biomass to remove undesirable material for further processing and applications. In some embodiments, the disclosure includes a biomass conditioning system including a conditioning tank, a water input device, a biomass input device, a containment device, a spillway, and a moving separation device. In some embodiments, methods according to the disclosure include pumping water into a conditioning tank, depositing biomass into the conditioning tank, allowing the biomass to soak in the water and separate into a bark portion and a non-bark portion, allowing the bark portion to float to a water line, containing the bark portion to one side of the conditioning tank, moving the bark portion into a bark storage area, separating the non-bark portion into a biomass portion and a debris portion, and moving the conditioned biomass portion into a storage area.