We conducted a microcosm experiment under near-natural conditions to investigate the effects of environmental stressors temperature and salinity on the response of three microalgal species. The response of microalgae to increased temperature and altered salinity is species-specific, with cell barrier complexity playing an important protective role. At decreasing salinity, the green flagellate cells of Dunaliella tertiolecta vibrate around the point and become stiff while their physiological activity is at its highest, which may indicate that organic matter is being released into the medium. At the highest salinity, Tetraselmis suecica showed the highest growth rate along with the hydrophobic behavior of the cells, which is a favorable condition for the formation of aggregates. Under these conditions, the cells could enter the cyst stage, while the content of polar lipids could mediate cell adhesion to the natural interfaces. Cylindrotheca closterium, a diatom with an organosilicate cell wall, also showed the highest physiological activity at decreasing salinity. However, the cells were softest and exhibited hydrophilic behavior, implying that released organic material could alter the surface properties of the diatom. This study provides insight into the behavioral, mechanical, and molecular changes of microalgae under near-natural conditions, which may contribute to a fundamental understanding of how biochemistry and mechanics interact to control the functional behavior of microalgal cells in climatically altered aquatic systems.