Development of cavity ring-down spectroscopy (CRDS) has enabled real-time monitoring of carbon stable isotope ratios of carbon dioxide and methane in air. Here we demonstrate that CRDS can be adapted to assess aquatic carbon cycling processes from microbial to ecosystem scales. We first measured in situ isotopologue concentrations of dissolved CO₂ (¹²CO₂ and¹³CO₂) and CH₄ (¹²CH₄ and ¹³CH₄) with CRDS via a closed loop gas equilibration device during a survey along an estuary and during a 40 h time series in a mangrove creek (ecosystem scale). A similar system was also connected to an in situ benthic chamber in a seagrass bed (community scale). Finally, a pulse-chase isotope enrichment experiment was conducted by measuring real-time release of ¹³CO₂ after addition of ¹³C enriched phytoplankton to exposed intertidal sediments (microbial scale). Miller-Tans plots revealed complex transformation pathways and distinct isotopic source values of CO₂ and CH₄. Calculations of δ¹³C-DIC based on CRDS measured δ¹³C-CO₂ and published fractionation factors were in excellent agreement with measured δ¹³C-DIC using isotope ratio mass spectroscopy (IRMS). The portable CRDS instrumentation used here can obtain real-time, high precision, continuous greenhouse gas data in lakes, rivers, estuaries and marine waters with less effort than conventional laboratory-based techniques.