We are trying with serial dilution and agar plating methods. The pH of the bloom is 8 and salinity is 10 ppt. Zarrouk's medium was used for isolation. The bloom is by the two cyanobacterial species Spirulina and Microcystis.
use tissue culture plates (6 wells per plate) with a few ml of the growth medium, with a pasteur pipette (elongated by heat) try to pick up one spirulina filament and diluted in the first well, do the same and dilute it in second well and so on till you have one filament per well., in this way you will isolate but also you will have a clonal culture of what you want.
You can try physical separation with the help of using difference in salinity. As both of them will not have the same specific gravity, slight increase or reduction will ensure their separation - I think, though have not used this technique.