Systems and methods are provided for synthesizing low nitrogen concentration organic liquids from biomass, such as algae, the organic liquids being suitable for refining into fuels and other chemicals. The biomass together with a solvent that is immiscible with water at room temperature are subjected to a subcritical hydrothermal treatment to disrupt cell structure and transform the biomass into a gas phase, a bio-oil phase, an aqueous phase and a solid phase. The aqueous phase contains most of the nitrogen. The resulting multiphasic mixture can be separated into four phases, including an aqueous phase and the organic liquid which consists of bio-oil dissolved in the solvent. Refined organic liquid can be recycled into the hydrothermal treatment as the solvent. The subcritical hydrothermal treatment can be performed at a generally low temperature and followed by a second hydrothermal treatment at a higher temperature.