The effects of climatic variables on lake‐water total organic carbon (TOC) concentrations and benthic and pelagic primary producers during the past 45 yr were assessed using the sediment records of two subarctic lakes, one with mires and one without mires connected to the lake. The lake with a mire showed large and synchronous changes in the planktonic to benthic (P : B) ratio of diatoms and concentrations of TOC inferred from nearinfrared spectroscopy. During periods of warm temperatures, high precipitation, and long ice‐free conditions, we inferred high TOC in the lake, and the diatom community was dominated by planktonic species. The stable carbon isotopic (Δ¹³C) values of sediment organic matter were negatively correlated with inferred TOC concentration and P :B ratio. We suggest that the changes in TOC and P : B ratio were a result of changing climate, permafrost degradation, and related changes in the catchment. Terrestrial organic matter, by its strong effect on the penetration of light through the lake water, possibly affected the habitats available for benthic photosynthesis and thus the Δ13C of the sediment organic matter. The large changes in recent times may also be because of unusually long ice‐free periods, warmer temperatures, and other associated limnological changes. The lake with no mire next to the lake showed only minor changes in lake‐water TOC during the same period and P :B ratio remained almost constant until the past 5 yr, when the P :B ratio increased rapidly. The observed changes in P :B ratio within this lake may be because of complex interactions of several climate‐related variables.