The process of eutrophication of water bodies, that is, the increase in the biological productivity of their ecosystems, has acquired such a large scale worldwide over the past few decades that today we are talking about lakes as “hot spots” of the carbon budget of the biosphere. Theoretical ideas about the mechanisms of functioning of aquatic ecosystems are needed to predict the emission of carbon dioxide from the surface of water bodies, as well as to assess their production and self-purification potential. However, the main provisions for theories on these issues have not been fully developed. In particular, the problem of nutrient limitation has not been solved. The phosphorus paradigm, which was dominant since the 1960s, underwent significant revision at the beginning of the 21st century, since the leading role of nitrogen in the control of the primary production process had been repeatedly shown. But there is no consensus on when an ecosystem is limited in nitrogen, when in phosphorus, or when co-limitation is observed. The article solves the question based on retrospective analysis of the state of production hydrobiology since the beginning of the 20th century, and studies performed over the last two decades on the nutrient limitation of aquatic ecosystems are analyzed. The broad ecological context of J. Liebig’s limiting factor principle and its biological meaning are also discussed. Most likely, each water body has a local set of conditions that ensures a change in the periods of nitrogen or phosphorus limitation of phytoplankton photosynthesis. Further studies of the problem of nutrient limitation should be aimed at elucidating the features of the interaction between algae and bacteria, in particular, the participation of bacteria in the nitrogen cycle and the destruction of organic compounds.