Reactions occurring at enzymes drive all of Earth’s biogeochemical cycles from the oxygen in the atmosphere to methane below the seafloor. Although these gases are critical for life on our planet, they have a multitude of sources and sinks that can be difficult to distinguish from one another, complicating our ability to understand their budgets both in the present and the past. Here, I explore new tracers of the oxygen and methane cycles with a focus on the biologic production and consumption of these gases: photosynthesis/respiration and methanogenesis/methanotrophy, respectively. Isotopes have been used as tracers of these processes since the inception of the field of stable isotope geochemistry, but only the measurement of singly-substituted molecules (i.e., 18O16O and 13CH4) has been possible. Within, I report measurements of the relative abundances of 18O18O and 18O17O for oxygen that has been biologically cycled in a terrarium experiment and respired in lake water as well as 13CH3D and 12CH2D2 of biologically produced and consumed subseafloor methane. These multiply-substituted isotopologues provide a new dimension of information by illuminating the enzyme level chemistry in making and breaking bonds. I find that photosynthesis and methanogenesis produce oxygen and methane respectively that is out of equilibrium with environmental temperatures and the resulting gases have fewer multiply-substituted isotopologues than predicted by chance alone. Respiration of oxygen leaves behind a residue enriched in these rare isotopologues; this unexpected result merits further exploration. However, anaerobic methanotrophy seems to be capable of reordering isotopes by enzymatic back reaction, driving a pool of methane to intra-species equilibrium at low temperature. These findings have consequences both for ongoing work in measuring marine primary productivity as well as exploring the extent of life in the deep biosphere and throughout the solar system.