Samples of sediment from lakes in Minnesota and Yellowstone National Park (YNP) were analyzed for organic carbon (OC), hydrogen richness by Rock-Eval pyrolysis, and stable carbon- and nitrogen-isotope composition of bulk organic matter. Values of δ¹³C of lake plankton tend to be around –28 to –32 parts per thousand (‰). Organic matter with values of δ¹³C in the high negative 20s overlap with those of organic matter derived from C3 higher terrestrial plants but are at least 10‰ more depleted in ¹³C than organic matter derived from C4 terrestrial plants. If the organic matter is produced mainly by photosynthetic plankton and is not oxidized in the water column, there may be a negative correlation between H-richness (Rock-Eval pyrolysis H-index) and δ¹³C, with more H-rich, algal organic matter having lower values of δ¹³C. However, if aquatic organic matter is oxidized in the water column, or if the organic matter is a mixture of terrestrial and aquatic organic matter, then there may be no correlation between H-richness and carbon-isotopic composition. Values of δ¹³C lower than about –28‰ probably indicate a contribution of bacterial biomass produced in the hypolimnion by chemoautotrophy or methanotrophy. In highly eutrophic lakes in which large amounts of ¹³C-depleted organic matter is continually removed from the epilimnion by photosynthesis throughout the growing season, the entire carbon reservoir in the epilimnion may become severely ¹³C-enriched so that ¹³C-enriched photosynthetic organic matter may overprint ¹³C-depleted chemosynthetic bacterial organic matter produced in the hypolimnon.

Most processes involved with the nitrogen cycle in lakes, such as production of ammonia and nitrate, tend to produce ¹⁵N-enriched values of δ¹⁵N. Most Minnesota lake sediments are ¹⁵N-enriched. However, some of the more OC-rich sediments have δ¹⁵N values close to zero (δ¹⁵N of air), suggesting that organic matter production is by nitrogen fixation, which further implies that nitrogen is limiting. Most lakes from YNP also have values of δ¹⁵N near zero.