The sedimentary data on two Yellowstone Lake sediment cores from 2016 - YL16-2C and YL16-5A, which include total organic carbon (TOC), total inorganic carbon (TIC), biogenic silica (BSi) concentrations, total nitrogen (TN) concentrations and carbon-nitrogen ratios (C/N) of the bulk sediment thought the Holocene. Furhter, stable silicon isotopes, and Ge/Si ratios of single endemitic diatom species Stephanodiscus yellowstonesis are included. Additionally, there are complete elemental composition data aquired using X-ray fluorescence (XRF) with an ITRAX and core logger data, including magnetic susceptibility measured ad LacCore Facility, Minneapolis, USA. Data on Yellowstone Lake water, Yellowstone Lake triburates and hydrothermal vents from two fields - West Thumb and Steavenson Island- include dissolved silicon, stable silicon isotopes and Ge/Si ratios sampled over period 2016-2018. All data were sampled to constrain the lake's silicon dynamics though out the Holocene and to identify sources of dissolved silicon in the lake. The sediment core analyzes of TOC, TN and C/N were measured on 5 to 10 mg of freeze-dried sediment using elemental analyzer COSTECH ECS4010 at Lund University, Sweden. The biogenic silica concentrations were determined using weak alkaline extraction by Conley and Schleske (2002, doi:10.1007/0-306-47668-1_14) using 30 mg of freeze-dried sediment reacting with 40 ml of 0.1M Na2CO3 for 5 hours. The DSi concentration in the extracted aliquot was measured using the molybdate-blue method (Strickland and Parsons, 1972) using Smarrtchem 200, AMS System discrete analyzer. Stable silicon isotopes were performed on leached cleaned diatoms (using NaOH) cation-exchange column cleaned (Georg et al., 2006; doi:10.1016/j.chemgeo.2006.06.006) samples using MC-ICP-MS at Vegacenter, Stockholm. Water samples for DSi and stable Si isotopes were sampled in HDPE acid-washed 125ml Nalgene bottles and filtered directly in the field through a 0.45μm Sterivex filter and further acidified using HCl to pH 2. DSi was analyzed by molybdate-blue method (Strickland and Parsons, 1972 (https://epic.awi.de/id/eprint/39262/1/Strickland-Parsons_1972.pdf)) using Smarrtchem 200, AMS System discrete analyzer. Stable silicon isotopes were performed on anion and cation-exchange column cleaned (Georg et al., 2006; doi:10.1016/j.chemgeo.2006.06.006, Gaspard et al. 2021; doi:10.1029/2021gc009904) samples using MC-ICP-MS at Vegacenter, Stockholm.