Immobilisation of algae by entrapment in alginate beads enables rapid nitrogen and phosphorus removal from wastewater and simplifies biomass harvesting for resource recovery. The alginate beads provide a protected environment for algal cultivation, enabling a species to be selected with less risk of contamination occurring during wastewater treatment. Immobilised Chlorella vulgaris, Scenedesmus abundans, Selenastrum capricornutum and Coelastrum microporum were compared in terms of the nutrient uptake capacity of each bead with the aim of selecting the species with highest uptake and so reducing the operational cost of bead generation. The N:P ratio assimilated from the wastewater varied markedly between species and was not affected by cultivation in N-depleted or P-depleted medium before immobilisation. This indicated species could be selected based on the relative importance of N or P removal for the site, or tailored to the wastewater, with C. vulgaris (cellular N:P of 6.1 ± 0.2) and S. abundans (2.6 ± 0.1) best suited for wastewater with a high and low N:P ratio, respectively. S. abundans adapted best to the restricted growth environment of the alginate matrix, assimilated the most P per cell (reducing interference of wastewater PO43− with the Ca-alginate structure), and thus led to the most durable beads during semi-continuous treatment of wastewater. This species gave the longest treatment duration of 42 days and algal cell production of 1.36 ± 0.7 × 107 cells/bead. S. abundans also achieved the greatest nutrient removal capacity (101 ± 8 μg N/bead and 45.9 ± 1.9 μg P/bead), demonstrating that the cost of alginate bead supply per unit of nutrient removed could be reduced and potential resource recovery from the biomass increased.