This research studied the effects of inorganic nutrient removal by free and immobilized Scenedesmus bijugatus cells, measured by algal growth (i.e., the chlorophyll a concentration) and the efficiency of the uptake of inorganic nutrients by the cells (uptake rate (b) and removal percentage) in water samples from the organically polluted Pinang River estuary (PRE). Water samples from the PRE were collected during low and high tide. S. bijugatus cells had a higher growth rate when incubated in low tide PRE water samples compared to high tide PRE water samples, with a growth rate of 0.29 µgml−1d−1 and 0.06 µgml−1d−1 for free and immobilized cells, respectively. S. bijugatus was able to more efficiently remove nitrogen, especially ammonium (81–94%), compared to phosphate (62–88%) from both low and high tide water samples. S. bijugatus cells in low tide PRE water samples recorded highest phosphate (0.36 mgL−1d−1 and 0.25 mgL−1d−1 for free and immobilized cells, respectively) and ammonium uptake rates (0.44 mgL−1d−1 and 0.29 mgL−1d−1 for free and immobilized cells respectively). Both inorganic nutrient removal and microalgal cell growth were not significantly different between free and immobilized S. bijugatus (p > 0.05). The data obtained indicated that the removal of nutrients by microalgae was affected by salinity and the immobilization technique applied may have good potential for bioremediation.