The stable carbon isotope composition of the carbonate encrustations (δ13CCARB), organic matter (δ13CORG) and the dissolved inorganic carbon (δ13CDIC) in the ambient lake waters were analysed for two common but morphologically different and, thus, representing different growth forms of Chara species. We hypothesized that the relationships between δ13CCARB, δ13CORG and δ13CDIC are species specific and related to the different growth forms of the studied charophytes. For each species (Chara tomentosa and Chara globularis), 10 individuals and water samples from above the macrophytes were collected in five lakes at three sites per lake in mid-summer. Opposing shifts were found between δ13CCARB and δ13CDIC values with 13C enrichment in C. tomentosa and 13C depletion in C. globularis. In addition, C. globularis exhibited more negative values of δ13CORG than C. tomentosa, even under similar conditions. The δ13CCARB and δ13CORG values were positively correlated in both species, but δ13CCARB and δ13CDIC as well as δ13CORG and δ13CDIC were positively correlated in C. tomentosa only. The differences found result from the different proportions between 13C and 12C in DIC used as a CO2 source for photosynthesis, which is linked to the different growth forms represented by the two studied charophytes and, thus, are species specific as we hypothesized.