We evaluated how eutrophication and humification impacted nutrient cycles and the efficiency of carbon transfer in the planktonic food webs of 12 lakes in north-eastern Poland that differed in trophic state. Our results indicated that the effectiveness of carbon transfer between phytoplankton and zooplankton varied from 0.0005% to 0.14%, which is much lower than the theoretical 10%. The highest efficiency of carbon transfer occurred in the mesotrophic lakes due to the higher hypolimnetic zooplankton production, while the lowest efficiency was observed in the dystrophic lakes and in one eutrophic lake that was dominated by cyanobacteria. Inedible algae (e.g. Gonyostomum semen) and cyanobacteria appeared to be the main factors reducing the efficiency of the transfer of matter in pelagic food webs. The results of our study showed that plankton communities are a key component of the nutrient cycle in freshwater food webs. Phytoplankton were a very effective nitrogen sink, and in the mesotrophic lakes, up to 99% of the total nitrogen was sequestrated in phytoplankton. As a result, there was a depletion of inorganic nitrogen in the upper water layer. Furthermore, zooplankton were an important phosphorus sink, thus significantly influencing the nutrient cycles.