This dataset contains stable silicon isotope measurements of radiolarian tests and sponge spicules analyzed by MC-ICP-MS. Isotopic differences between radiolarian size fractions and morphotypes were also examined. The data contribute to a broader study aimed at reconstructing the marine silicon cycle during the Middle Eocene Climatic Optimum (MECO) in order to investigate changes in silicate weathering feedbacks and ocean circulation, using siliceous microfossils from IODP Site U1511, ODP Site 1260, and ODP Site 1051.