Schoell has made many contributions to geochemistry with emphasis on the applications of stable isotope analysis. The results of Schoells work have included identifying the pathways of formation that distinguish methane of biogenic origin from that of thermogenic origin using stable isotope analysis. In the paper, "Biogenic methane formation in marine and freshwater environments: CO reduction VS. acetate fermentation-Isotope evidence", Schoell et al. identify that the two primary methods for aquatic and marine methane production are carbon dioxide reduction and acetate fermentation, respectively. By recognizing the difference in δC and δD fractionation of the water environments and observing the differences in δC and δD fractionations of the methane product, Schoell et al. concluded that the dominant pathway of methane in marine environments is via acetate fermentation, while methane in freshwater environments arises from CO reduction. By analyzing the CH and HO fractionation, Schoell, et al.' offer a technique for identifying the original environment in which methane was produced.
Schoell continued his work with methane origin studies expanding his research to consider how stable isotopes can provide insight regarding the temperature of the environment for both thermogenic and biogenic methane production. Specifically, Schoell collaborated on the paper "Formation temperatures of thermogenic and biogenic methane" authored by D. Stolper, which used "clustered isotope" techniques to determine the temperature at which methane was produced. This approach has become useful for identifying the thermal conditions of methane formation for both the high temperatures of thermogenic methane production and the relatively lower temperatures of microbial methane production as well as characterizing the contribution of both producers to a mixed sample.
While the majority of Schoell's work has revolved around identifying the origins and pathways of methane production, he has also done work using stable isotope analysis to address how environmental factors affect preservable products of biological activity. Schoell addresses this topic in the paper, "Sensitivity of biomarker properties to depositional environment and/or source input in the Lower Toarcian of SW-Germany". In addition to this, his career has included the research of how stable isotope analysis can be used to identify the mixing and composition of natural gasses, as discussed in "Use of Gas Isotope Analyses for Reservoir Management".