Combined measurements of salinity and the oxygen/hydrogen stable isotope composition of marine waters can characterise processes such as freshwater mixing, evaporation, precipitation and sea-ice formation. However, stable isotope data with high spatial and temporal resolution are necessary for a detailed understanding of mixed water bodies with multiple inputs. So far analysis of δ18O and δD values in water has been a relatively expensive, laboratory-based technique requiring collection of discrete samples. This has greatly limited the scope and scale of field research that can be undertaken using stable isotope analysis. Here, we report the first continuous shipboard measurements of δ18O and δD values in water by diffusion sampling-cavity ring-down spectrometry. Combined with continuous salinity recordings, a data set of nearly 6,000 measurements was made at 30-s intervals during a 3-day voyage through the Great Barrier Reef Lagoon. Our results show that continuous shipboard measurement of δ18O/δD values provides additional discriminatory power for assessing water mass formation processes and histories. Precise identification of river plumes within the Great Barrier Reef Lagoon was only possible because unique δ18O/δD–salinity relationships of individual plumes were measured at high spatial and temporal resolution. The main advantage of this new technique is the ability to collect continuous, real-time isotope data at a small fraction of the cost of traditional isotope analysis of discrete samples. Water δ18O and δD values measured by diffusion sampling-cavity ring-down spectrometry and laboratory-based isotope ratio mass spectrometry have similar accuracy and precision.