System and method for determining total inventory of batch and continuous biomass inventories in a biofuel production process. Measured biomass inventory values are received, including batch inventories from multiple batch fermenters and at least one continuous beer well inventory. The values are premised on a controlled vapor pressure of the batch fermenters and beer well(s), where the pressure fluctuates in an uncontrolled manner. A measured vapor pressure for the batch fermenters and beerwell(s) is received, and pressure compensated inventory values determined based on the measured inventory and pressure values. Measured biomass input flow to the batch fermenters and output flow from the beerwell(s) are received, and are premised on a constant biomass temperature and density, where biomass temperature and density fluctuate in an uncontrolled manner. The total inventory of batch and continuous inventories is determined based on the measured flows and the pressure compensated inventory values, and stored.