This dataset includes ion concentrations and isotopic compositions (δ³⁰Si and ⁸⁷Sr/⁸⁶Sr) derived from a two-year sediment incubation experiment. The experiment involved overlying water, porewater, sediment, and substrate samples. Sediment samples were collected from the Severn Estuary catchment (51°37'53.1"N, 2°38'52.1"W), and the overlying water was sourced from an upstream tributary (51°47'05.8"N, 2°40'26.2"W). Samples were retrieved after one year and two years of incubation to investigate geochemical and isotopic changes over time. Sediment samples underwent sequential chemical leaching to extract three operationally defined silicon (Si) pools: Si-HCl (reactive silica), Si-Alk (amorphous biogenic or authigenic silica), and Si-NaOH (lithogenic silica with refractory biogenic silica and authigenic clay). In addition, both carbonate and silicate fractions were extracted to assess their respective ⁸⁷Sr/⁸⁶Sr ratios. To simulate typical mineral phases found in estuarine systems, five substrates were used in the incubation: kaolinite, quartz, iron-coated quartz, glass beads, and iron-coated glass beads.