Phytoremediation technologies are employed worldwide to remove nutrient pollutants from agricultural and industrial wastewater. Unlike in algae-based nutrient removal, control methodologies for plant-based remediation have not been standardized. Control systems that guarantee consistently low outlet concentrations of nitrogen and phosphorous often use expensive analytical instruments and are therefore rarely viable. In this study, pH measurement was used as the sole input to control the nitrate outlet concentration in a continuously operated Lemna minor (lesser duckweed) phytoremediation tank. When grown in 20 L batches of modified Hoagland’s solution, it was found that a constant ratio exists between the amount of nitrate removed and the amount of acid dosed (required for pH control), which was equal to 1.25 mol N·(mol H+)−1. The nitrate uptake rates were determined by standard spetrophotometric method. At critically low nitrate concentrations, this ratio reduced slightly to 1.08 mol N·(mol H+)−1. Assuming a constant nitrogen content, the biomass growth rate could be predicted based on the acid dosing rate. A proportional-integral controller was used to maintain pH on 6.5 in a semi-continuously operated tank covered by L. minor. A nitrogen control strategy was developed which exploited this relationship between nitrate uptake and dosing and successfully removed upwards of 80% of the fed nitrogen from synthetic wastewater while a constant biomass layer was maintained. This study presents a clear illustration of how advanced chemical engineering control principles can be applied in phytoremediation processes.