Most of the aquatic vegetation produces organic substances via the C3 photosynthetic pathway (mosses, isoetids-Lobelia dortmanna L., Luronium natans (L.) Raf., and vascular plants) or Crassulacean acid metabolism (CAM, e.g., Littorella uniflora (L.) Asch. and Isoëtes lacustris L.) or by their ability to use HCO3- via carbon concentration mechanisms (CCMs-some elodeids and charophytes). Differentiating these predominant photosynthetic pathways in aquatic vegetation based on their organic matter (OM) carbon stable isotopes (δ13CORG) is a complex task, in contrast to terrestrial plants. This study investigates the OM deposition, characterized by δ13CORG values in 10 macrophyte species with different photosynthetic pathways (C3, CAM, and CCM) collected from 14 softwater Lobelia lakes in northern Poland. The higher δ13CORG values distinguish the CCM group, indicating their use of 13C-enriched HCO3¯ in photosynthesis. CAM species show slightly higher δ13CORG values than C3, particularly in lower pH lakes. Principal component analysis of isotopic and environmental data did not yield clear distinctions by the groups, but still, they significantly differ in light of analyzed parameters and isotopic signals (PRMANOVA = 5.08, p < 0.01; K-W H = 27.01, p < 0.001). The first two PCA dimensions showed that the water pH and Ca2+ concentration positively influenced δ13C values. The influence of light conditions on δ13CORG values revealed by third PCA components seems to also be important. In summary, northern Polish Lobelia lakes serve as a key differentiation point between vegetation employing CCMs and those relying on C3/CAM photosynthesis without HCO3- utilization, providing insights into transitions in plant communities within these ecosystems.