Hydrothermal processing may provide an attractive alternative for producing biofuels with microalgae. Hydrothermal processing can be used with wet feedstocks without needing energy-intensive drying or solvents for oil recovery as is typical for algae biofuel processes. In this study, microalgae strains Isochtysis sp. and Thalassiosira weissflogii were processed in a hydrothermal batch reactor at temperatures of 250-350 degrees C and residence times up to 3 h. Triglyceride feedstock hydrolysis in hydrothermal systems was modeled using previously identified methods. Kinetic parameters for triglyceride hydrolysis were fit to literature data. Degradation of unsaturated fatty acids in hydrothermal systems was modeled by adding reaction pathways to the hydrolysis reaction system, and fitting kinetic parameters to the experimental data. The time scale for the degradation indicates that short reaction times (<30 min) with high temperatures (300-350 degrees C) will maximize the yield of free fatty acids before degradation occurs.