The teleconnections existing between low- and high-latitude water masses are a critical component of the Earth’s climate system. One region of global significance is the Indian-Atlantic Ocean gateway (I-AOG) that lies off the southern tip of Africa. Today, the regional oceanography is dominated by the Agulhas Current and its leakage into the South Atlantic, the so-called “warm water route,” the Agulhas Current Retroflection and the Agulhas Return Current’s interaction with the subtropical front (STF). However, the connections between these frontal systems and links to high latitude climate dynamics are not well understood. On glacial/interglacial timescales, biogenic silica (BSi) production in the I-AOG, close to the STF, has been linked to transport of high-latitude silica rich intermediate waters to this site throughout the Pleistocene (Romero et al., 2015). Here we present BSi accumulation rates, diatom assemblage data, and bulk sediment chemistry (XRF) for Pliocene age sediments from IODP Site U1475 (41°25.61’S; 25°15.64’E, 2669 m water depth). While the overall BSi content remains low (0.5 to 4.18 weight %), increases in diatom accumulation are seen at four distinct intervals (4.6 to 4.3 Ma, 3.3 Ma, 3.14 Ma, and 2.8 to 2.6 Ma). Additionally, XRF records of Si/Al and Ba/Al appear to coincide with the BSi record and we infer that nutrient-rich intermediate waters “leaked” from the Southern Ocean and resulted in increased BSi production. Additionally, an increase in opal accumulation at the Site between 4.6 to 4.3 Ma, is likely tied to a reorganization of global nutrient pools associated with the shoaling of waters at the Panama Canal. During the shoaling event BSi production increases at Site U1475 are coincident with a reduction in BSi production in the Galapagos Basin (e.g. ODP Site 846), thus suggesting a potential connection between Pacific and Atlantic Ocean basins during the Pliocene. An increase in abundance of Southern Ocean diatoms from 3.9 Ma to 2.6 Ma may also indicate water mass cooling and increased transport of high-latitude intermediate waters. The Site U1475 record of microfossils highlights a trend of intermediate water input throughout the Pliocene. Additionally, comparisons with the so-called “cold water route” will allow a better view of global intermediate water changes during the Pliocene.