The aim of this study was to assess vertical and seasonal variations of inorganic carbon allocation into macromolecules by phytoplankton population in an humic and acidic lake (Lake Vassiviere) and in a clearwater lake (Lake Pavin). Biochemical fractionation was done by consecutive differential extractions in order to separate proteins, polysaccharides, lipids and low molecular weight compounds (LMW) by virtue of their relative solubilities in different extraction solvents. Independent of depth and season, the principal photosynthetic end products were polysaccharides followed by proteins, LMW and lipids. However, inorganic carbon allocation into macromolecules varied, in these two lakes, with depth and with the taxonomic composition of phytoplankton. Carbon allocation into polysaccharides decreased with increasing depth, especially in the brown-colored humic lake, and Diatoms showed high C incorporation into polysaccharides.