The effects of temperature, salinity, and illumination on the nitrite uptake rate of the microalgae–bacteria consortia of Oocystis borgei and Rhodopseudomonas palustris were investigated. The absorption rates of nitrite and the contribution rate of each component in the consortia under different temperatures (15, 20, 25, 30, 35 °C), illuminations (0, 15, 25, 35, 45 μmol·m−2·s−1), and salinities (0, 5, 15, 25, 35‰) were determined by stable isotope labeling technique. The single and combined effects of three environmental factors on nitrite uptake by the microalgae–bacteria consortia were analyzed using single-factor and orthogonal experiments. The single-factor experiment showed that the microalgae–bacteria consortia could absorb nitrite efficiently when the temperature, salinity, and illumination were 20~30 °C, 0~15‰, and 25~45 μmol·m−2·s−1, respectively, with the highest absorption rates were 2.086, 3.058, and 2.319 μg∙g−1∙h−1, respectively. The orthogonal experiment showed that the most efficient environmental conditions for nitrite uptake were 30 °C, 5‰ salinity, 35 μmol·m−2·s−1 illumination, and the rate of nitrite uptake by the microalgae–bacteria consortia was 3.204 μg∙g−1∙h−1. The results showed that the nitrite uptake rate of the O. borgei–R. palustris consortia was most affected by temperature, followed by salinity, and least by illumination. Under the same conditions, the nitrite absorption capacity of the microalgae–bacteria consortia was greater than that of single bacteria or algae, and R. palustris played a major role in the nitrite absorption of the consortia. The O. borgei and R. palustris consortia still maintain high nitrite absorption efficiency when the environment changes greatly, which has broad application prospects in the regulation and improvement of water quality in shrimp culture.