Ecological research using stable isotopes has progressed rapidly during the last 20 years and although more studies are including the addition of isotopically labelled compounds at tracer levels, the overwhelming majority rely on measurements of natural abundance ratios. Access to isotope ratio mass spectrometry has increased, spurred on by awareness of the techniques and increasing demand, and consequently cost of sample analysis has dropped. Today stable isotopes of carbon (¹³C/¹²C), nitrogen (¹⁵N/¹⁴N), sulphur (³⁴S/³²S), oxygen (¹⁸O/¹⁶O), and hydrogen (²H/¹H) can be determined routinely. Perhaps one of the most appealing attributes of isotopic signatures is their potential use to find patterns and determine mechanisms across a range of scales from the molecular level through to characterising whole food webs, reconstructing palaeoenvironments, tracing nutrient fluxes between ecosystems and identifying subsidies, or migrations of organisms. Ecologists from every discipline who are unlikely to have been trained as isotope chemists have added stable isotope analysis (SIA) to their “toolbox”, but often increasing use leads to increasing abuse. The usefulness of SIA arises from predictable physical and enzymatic-based discrimination between biological and non-biological materials leading to different isotopic compositions. Without some ecological understanding of these, interpretation of isotope-derived data can often be flawed. Here, I explore how SIA recently has been used for research in aquatic ecology, reviewing how some of these techniques have allowed elucidation of key processes in aquatic systems such as the contribution of allochthony to lake food webs, and discuss the “state of the art”. Included are some thoughts on where our knowledge in aquatic ecology remains deficient and how continued development and future application of SIA and interdisciplinary methodologies may be applied.
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