Silicon isotope ratios (expressed as δ30Si) in marine microfossils can provide insights into silica cycling over geologic time. Here we used δ30Si of sponge spicules and radiolarian tests from the Paleogene Equatorial Transect (Ocean Drilling Program Leg 199) spanning the Eocene and Oligocene (~50–23 Ma) to reconstruct dissolved silica (DSi) concentrations in deep waters and to examine upper ocean δ30Si. The δ30Si values range from −3.16 to +0.18‰ and from −0.07 to +1.42‰ for the sponge and radiolarian records, respectively. Both records show a transition toward lower δ30Si values around 37 Ma. The shift in radiolarian δ30Si is interpreted as a consequence of changes in the δ30Si of source DSi to the region. The decrease in sponge δ30Si is interpreted as a transition from low DSi concentrations to higher DSi concentrations, most likely related to the shift toward a solely Southern Ocean source of deep water in the Pacific during the Paleogene that has been suggested by results from paleoceanographic tracers such as neodymium and carbon isotopes. Sponge δ30Si provides relatively direct information about the nutrient content of deep water and is a useful complement to other tracers of deep water circulation in the oceans of the past.