50 samples were taken at 0.02 m depth intervals from the uppermost metre of the core RAPiD-21-03K to cover the past ~800 years with approximately 8-year resolution, for the quantification of silica mass in diatom frustules. 60 Coscinodiscus spp. tests per sample were isolated and their silica mass contents measured using ICP-mass spectrometry. In this dataset, 'depth' is the midpoint distance each sediment sample was taken from the top of the core in m, 'age' is the calibrated age in both years before present and in common era calendar years, '# Diatoms' is the number of diatom valves in each 0.5 mL sample to be measured, 'Si 28 concentration' is the measured total concentration of silicon-28 in each 0.45 mL sample aliquot in µg/L, 'blank corrected Si' is the total silicon-28 concentration minus the average blank value in µg/L, 'SiO2/diatom' is the blank corrected silicon-28 concentration scaled up from 0.45 mL to 0.5 mL, scaled from Si to SiO2, and divided by the number of diatoms per sample in ng, 'isoutlier' identifies values more than three scaled median absolute deviations from the median.