In this paper we approach the problem of the origin of organic‐carbon‐rich sediments by using an integrated isotopic and organic geochemical study of the annual productivity/eutrophication cycle in the water column of Lake Greifen (Switzerland) and the historical expression of such cycles as found in the sediments. The Lake Greifen water column and sediment studies reveal that Δδ13C carbonate‐organic matter is correlated with the hydrogen indices (HI) of kerogens, explicable in terms of changing productivity and preservation of the organic matter, and the CO2budget of the water body. The lake model implies that, if high productivity in CO2limited surface waters (high nutrient/CO2ratio) was controlling the preservation of organic matter, a correlation between decreasing Δδ13C carbonate ‐organic matter and increasing HI values may be observed. In contrast, if low to moderate productivity in CO2unlimited surface waters (low nutrient/CO2ratio) where bottom water anoxia promotes the preservation of organic matter, a correlation between increasing Δδ13C carbonate‐organic matter and increasing HI values may be observed. Application of this model to two well known Jurassic sequences, gave a correlation of increasing HI values with decreasing Δδ13C carbonate‐organic matter for the Kimmeridge Clay Formation (United Kingdom), and increasing HI values with increasing Δδ13C carbonate organic matter for the early Toarcian shales (France). This suggests that the controlling factor of the former deposit was high primary bioproductivity and of the latter deposit anoxic bo