Microalgae are very efficient at removing nutrients from municipal wastewater and may be a viable tertiary wastewater treatment while additionally improving the economics of microalgal cultivation for biofuel production. The relative quantities and productivities of fatty acids, carbohydrates and proteins were determined in the microalga Scenedesmus sp. AMDD grown in treated municipal wastewater in continuous chemostats under different dilution rates or hydraulic retention times. The dilution rate of the chemostat exerted a strong control over the biochemical composition of the cultivated biomass and clear differences in the patterns of accumulation of cellular constituents were detected. Maximum carbohydrate and protein productivities were estimated to be 130 and 120mgL−1d−1, respectively, at dilution rates of 0.5d−1 and 1.05d−1, respectively. Fatty acid productivity was fairly constant at about 20mgL−1d−1 across all tested dilution rates. Total fatty acid only accumulated when growth rates were very low or when a prolonged nutrient starvation regime was imposed by interrupting the supply of wastewater to the chemostat. Monounsaturated fatty acids increased by 250%, whereas polyunsaturated fatty acids decreased by 60% and saturated fatty acids remained fairly constant, from the highest dilution rate of 1.05d−1 to nutrient starved cells. The rate of wastewater nutrient remediation therefore strongly controls the composition of the biomass, thereby controlling its commercial applicability.