Phytoplankton present in the marine and estuarine environments use carbon dioxide for photosynthesis and hence play an important role in maintaining the carbon dioxide budget of the atmosphere.
My view is that you should adopt a minimal DESTRUCTIVE PROCEDURE for estimating STORED carbon.It is possible to estimate by obtaining known portion of material from phyto planktons (may range from mg to g or even 100 gms) precisely weighed and employ appropriate COMBUSTION technique with controlled Temperature.Later find out Mass of Carbon from the Green dry matter and later extrapolate carefully with established allometric Biomass estimators of that particular Phyto plankton.
Just put the plankton in an NMR tube and determine the proportion of Carbon. (and other components you may be interested in). Then weigh the total tube contents so you can determine the weight of each component you have identified with FT-NMR.
The determination of starch or glycogen (for cyanobacteria) accumulated in photosynthetic cells could be useful. In stationnary phase which often corresponds to the decrease of some element such nitrogen in the medium, some cyanobacteria synthetise polysaccharides.