Analyses of the natural variation in stable isotopes of components of ecological systems have provided new insights into how these systems function across paleoecological to modern timescales and across a wide range of spatial scales. Isotope abundances of the molecules in biological materials and geochemical profiles are viewed as recorders that can be used to reconstruct ecological processes or to trace ecological activities. Here, we review key short-, medium- and long-term recording capacities of stable isotopes that are currently being applied to ecological questions. The melding of advances in genetics, biochemical profiling and spatial analysis with those in isotope analyses and modeling sophistication opens the door to an exciting future in ecological research.