Aragonitic clathrites are methane-derived precipitates that are found at sites of massive near-seafloor gas hydrate (clathrate) accumulations at the summit of southern Hydrate Ridge, Cascadia margin. These platy carbonate precipitates form inside or in proximity to gas hydrate, which in our study site currently coexists with a fluid that is highly enriched in dissolved ions as salts are excluded during gas hydrate formation. The clathrites record the preferential incorporation of 18O into the hydrate structure and hence the enrichment of 16O in the surrounding brine. We measured δ18O values as high as 2.27‰ relative to Peedee belemnite that correspond to a fluid composition of −1.18‰ relative to standard mean ocean water. The same trend can be observed in Ca isotopes. Ongoing clathrite precipitation causes enrichment of the 44Ca in the fluid and hence in the carbonates. Carbon isotopes confirm a methane source for the carbonates. Our triple stable isotope approach that uses the three main components of carbonates (Ca, C, O) provides insight into multiple parameters influencing the isotopic composition of the pore water and hence the isotopic composition of the clathrites. This approach provides a tool to monitor the geochemical processes during clathrate and clathrite formation, thus recording the evolution of the geochemical environment of gas hydrate systems.