Species specific nitrogen-to-phosphorus molar ratio (NPR) has been suggested for green microalgae. Algae can store nitrogen and phosphorus, suggesting that the optimum feed concentration dynamically changes as function of the nutrient storage. We assessed the effect of varying influent NPR on microalgal cultivation in terms of microbial community stability, effluent quality and biokinetics. Mixed green microalgae (Chlorella sorokiniana and Scenedesmus sp.) and a monoculture of Chlorella sp. were cultivated in continuous laboratory-scale reactors treating used water. An innovative image analysis tool, developed in this study, was used to track microbial community changes. Diatoms proliferated as influent NPR decreased, and were outcompeted once cultivation conditions were restored to the optimal NPR range. Low NPR operation resulted in decrease in phosphorus removal, biomass concentration and effluent nitrogen concentration. ASM-A kinetic model simulation results agreed well with operational data in the absence of diatoms. The failure to predict operational data in the presence of diatoms suggest differences in microbial activity that can significantly influence nutrient recovery in photobioreactors (PBR). No contamination occurred during Chlorella sp. monoculture cultivation with varying NPRs. Low NPR operation resulted in decrease in biomass concentration, effluent nitrogen concentration and nitrogen quota. The ASM-A model was calibrated for the monoculture and the simulations could predict the experimental data in continuous operation using a single parameter subset, suggesting stable biokinetics under the different NPR conditions. Results show that controlling the influent NPR is effective to maintain the algal community composition in PBR, thereby ensuring effective nutrients uptake.