Microalgae can remove nutrients and organic contaminants from municipal wastewater reverse osmosis concentrate (ROC) and enable resource recovery via biomass production. Two cationic starch flocculants (starch-graft-poly cationic moiety 2-methacryloyloxyethyl trimethyl ammonium chloride (St-g-PDMC) and starch-graft-poly cationic moiety 2,3-epoxypropyl trimethyl ammonium chloride (St-GTA)) were synthesized and tested as potential greener and lower cost alternatives to conventional chemical flocculants for harvesting Chlorella vulgaris and Nannochloropsis salina from the algae-treated ROC. St-GTA achieved up to 97% separation (based on optical density) for both algal species at the dosage of 5–10 mg g−1 dry cell weight (DWC) compared to alum (69% at 10 mg g−1 DWC) and PolyDADMAC (93% at 35 mg g−1 DWC). The overall better performance of St-GTA was attributed to its higher intrinsic viscosity, positive surface charge, and solubility. The harvesting efficiency was influenced by algal growth phases, which led to differences in the levels of negative charge and functional groups on the algal surfaces. The effectiveness of the flocculants was primarily associated with their respective level of positive surface charge (R2 = 0.87) that facilitated charge neutralization as indicated by apparent surface charge of the algal flocs (R2 = 0.97). Flocculation using St-GTA removed 40% TP, 25% TN, and 20% DOC from the residual contaminants of the algae-treated ROC. Overall, the study indicated that cationic starch could be an environmentally benign and cost-effective approach for harvesting microalgae from the treated ROC, and beneficial to the subsequent utilization of the harvested biomass.