The stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen (13C/12C, 15N/14N, 18O/16O, and 2H/1H) in the organic molecules of an organism are a consequence of its physiology and growth environment. For example, the carbon isotope ratio of cellulose is a consequence both of the plant's physiology (whether it fixes carbon by the C3, C4, or CAM pathway) and the environmental water stress it experiences, which affects the diffusion of carbon dioxide in and out of its leaves. The carbon isotope ratio of a heterotroph is a consequence of the carbon isotope ratio of its dietary constituents. Because of these causative relationships, stable isotope ratios can provide information about an organism's growth environment and/or nutrient sources, and have been used for such applications as elucidating food webs, reconstructing climate, and linking migratory animal populations to natal origins.

The stable isotope ratios of organic constituents of microorganisms also reflect those of their growth environments, which include both nutrients and water. Thus genetically identical microorganisms growing on isotopically distinct substrates can be differentiated through their stable isotope ratios. In the case of laboratory-grown organisms, isotopic correlations can link cultures to growth media and water, providing potential forensic information. In the environment, stable isotope ratios can reveal the flow of isotopically distinct nutrients through a community and may be useful as natural tracers for nutrient inputs. Isotopic approaches combined with DNA or fatty acid analysis can be applied to identify microbes within a consortium that process a specific type of substrate. Stable isotopes thus act as natural tracers for following the flow of elements through the environment, and isotope ratio analysis offers a powerful complement to genetic analysis in understanding environmental microbial dynamics.