Silicon (Si) is an essential macronutrient for diatoms, an important component of lacustrine primary productivity that represents a link between the carbon and silicon cycles. Reconstructions of lake silicon cycling thus provide an underexploited window onto lake and catchment biogeochemistry. Silicon isotope geochemistry has potential to provide these reconstructions, given the competing source and process controls can be deconvolved. The silica-rich volcanic and hydrothermal systems in Yellowstone National Park are a great source of dissolved silicon into Yellowstone Lake, a system with high silicon, and thus carbon, export rates and the formation of diatom–rich sediment. Yellowstone Lake sediments should be an archive of past silicon biogeochemistry, although the effect of sublacustrine hydrothermal activity or hydrothermal explosion events is unclear.Here, we analysed lake water, tributaries, and hydrothermal vent fluids from Yellowstone Lake for their dissolved Si concentrations, isotope composition (δ30Si) and Ge/Si ratios to evaluate the sources of variability in the lake's Si cycle. Bulk elemental composition and biogenic SiO2 (bSiO2) content, together with δ30Si and Ge/Si ratios from a single diatom species, Stephanodiscus yellowstonensis, were analysed in two sediment cores spanning the last 9880 cal. yr BP. We investigate these datasets to identify long term Holocene changes in hydrothermal activity and effects of large and short-term events i.e., hydrothermal and a volcanic eruption.Combinations of bSiO2, δ30Si and Ge/Si with XRF and lithology data revealed that Yellowstone Lake has a resilient biogeochemical system: hydrothermal explosions are visible in the lithology but have no identifiable impact on bSiO2 accumulation or on the δ30Si signature. Both cores show similarities that suggest a stable and homogeneous dSi source across the entire lake. A narrow range of δ30Si and Ge/Si values suggests that the productive layer of the lake was well mixed and biogeochemically stable, with consistently high hydrothermal inputs of Si throughout the Holocene to buffer against the disturbance events. Variation in bSiO2 concentration through time is weakly correlated with an increase towards younger sediment in the δ30Si fossil diatom record in both cores. This increase mirrors that seen in ocean records, and follows changes known in summer insolation, summer temperatures and lake water-column mixing since the deglaciation. This suggests that climate forcing, and soil formation ultimately govern the silicon isotope record, which we suggest is via a combination of changes in weathering stoichiometry, diatom production, and relative proportion of dSi sources.