Chemical and isotopic changes in plant biochemicals that were transformed into organic geochemicals have been measured in anaerobic, freshwater marsh environments. In two litter bag studies, plant biochemicals decayed extenzively in the first year, as recorded by dry weight, C:N ratios, 15N of bulk tissue and amino acids, and 13C of individual amino acids. Molecular analyses of Rubisco revealed that the high-molecular-weight enzyme subunit could be recognized antogenically for at least 12 months, but concentrations and amound declined. Geochemical compounds, advanced glycation endproducts, were not found in fresh plants, but formed gradually with first indications documented at 3 months. The organic remains of plants were reworked or replaced by microbial products from decomposition, as indicated by a shift in the isotopic composition of individual amino acids in total plant protein. In experiments with Rubisco, isotopic changes over time in the individual amino acids in the 50-60 kDa molecular weight range were substantial. These high-molecular-weight substances were no longer pristine molecules. Biochemical and isotopic tools for studying living processes have been demonstrated to be effective and novel approaches to identify and quantify altered geochemical remnants.