System and method for managing fermentation feed in a biofuel production process, comprising a dynamic multivariate predictive model-based controller coupled to a dynamic multivariate predictive model. The model is executable to: receive process information, including water inventory and biomass information, from the biofuel production process; receive a specified objective for the fermentation feed specifying a target biomass concentration; and generate model output comprising target values for a plurality of manipulated variables of the biofuel production process, including target flow rates of water and/or biomass contributing to the fermentation feed in accordance with the specified objective. The controller is operable to dynamically control the biofuel production process by adjusting the plurality of manipulated variables to model-determined target values to stabilize water/biomass balance in the fermentation feed in accordance with the specified objective, including the specified target biomass concentration.