jats:titleAbstract</jats:title>jats:pAn accurate description of the carbonate system in pore waters is valuable in studies involving the degradation of sedimentary organic matter, recrystallization of calcium carbonate minerals, calculations of mineral saturation state, and cycling of ions affected by pH. Here, we analyze water chemistry of pore water extracted using centrifugation and Rhizon samplers from hemipelagic sediments in the Gulf of Aqaba, Red Sea, and a shallow salt marsh from Norfolk, England. In both study areas, the data are internally consistent for each pore‐water separation technique, but the measured isotopic composition of the dissolved inorganic carbon (δjats:sup13</jats:sup>Cjats:sub[DIC]</jats:sub>) differs between the two techniques. We performed laboratory experiments that show that both Rhizons and centrifugation are prone to degassing of COjats:sub2</jats:sub> enriched with jats:sup12</jats:sup>C. We suggest that during sampling with Rhizons, air fills the voids left by extracted pore water; combined with the membrane's design to exclude air, some of the aqueous COjats:sub2</jats:sub> diffuses into these air bubbles instead of the sampler. Rhizons produce reliable calcium, strontium, manganese, and barium concentration data when soaked in deionized water and then flushed with the sample immediately prior to sampling. However, pore‐water extractions with Rhizons are less reliable for analyses of pH and δjats:sup13</jats:sup>Cjats:sub[DIC]</jats:sub>. Centrifugation produces reliable carbonate chemistry and major element data when tubes are fully filled without headspace and sealed tightly. Working in COjats:sub2</jats:sub> low/free atmosphere (e.g., Njats:sub2</jats:sub> glovebox) enhances the chance of losing COjats:sub2</jats:sub> from the sample in both sampling techniques due to increased negative gradient of COjats:sub2</jats:sub> between the core and its surrounding.</jats:p>