System and method for determining total mill flow (TMF) in a biofuel production process. Measured slurry flow and density values from a process fed by mill(s), backset, and at least one water source, are received. The slurry includes biomass solids and water. Measured backset flow and density values, and a backset composition value are received, as well as a slurry composition value indicating % biomass solids of the slurry is received. A quantity of biomass solids and/or water of the slurry determined based on the slurry flow, density, and composition, and a quantity of the biomass solids and/or water of the backset determined based on the backset flow and density, backset composition, and a system filter characterizing time delays and lags between measurements of the backset flow and biomass slurry flow. Total mill flow is determined based on the quantities of biomass solids and/or water of the slurry and backset.