Abstract: Integrated biorefineries are provided that integrate biomass cultivation with processing to convert cultivated biomass to a fuel, and further integrate carbon recovery from the biomass processing. Biomass processing to fuels begins in a treatment system, such as a hydrothermal treatment system, that produces an organic phase that is suitable for refining to a fuel and also produces a waste stream. The biorefinery optionally includes a dewatering system, a refining system to convert the organic phase to the fuel, and a cogeneration system configured to use at least some of the fuel produced by the treatment system to generate electricity and heat that can be used for biorefinery operations.