You are correct that chl. a is not a perfect indicator or algal biomass since it varies greatly with time of day, physiological state of the algae etc. However people often use conversion factors based on Chl. a or use mean C contents of certain plankton groups. For example heterotrophic marine bacteria have an average C content of ~20 fg/cell while cyanobacteria roughly have 200 fg/cell. I have used these numbers to estimate the relative carbon contribution of each group from cell counts using a flow cytometer. I have also used a generic 60:1 carbon to chl a ratio which has been used by several people to normalize primary production rates etc. in the absence of actual particular organic carbon data. The references are in my paper Koch et al. 2012, Vitamin B1 and B12 uptake and cycling by plankton communities in coastal ecosystems, Frontiers in Microbiology, Volume 3. Let me know if i can assist you further.

thank you so much Mr Koch