The trace element composition of planktic foraminifera shells is influenced by both environmental and biological factors (‘vital effects’). As trace elements in individual foraminifera shells are increasingly used as paleoceanographic tools, understanding how trace element ratios vary between individuals, among species, and in response to high frequency environmental variability is of critical importance. Here, we present a three-year plankton tow record (2010–2012) of individual shell trace element (Mg, Sr, Ba, and Mn) to Ca ratios in the planktic species Globigerina ruber (pink), Orbulina universa, and Globorotalia menardii collected throughout the upper 100 m of Cariaco Basin. Plankton tows were paired with in situ measurements of water column chemistry and hydrography. The Mg/Ca ratio reflects different calcification temperatures in all three species when calculated using species-specific temperature relationships from single-species averages of Mg/Ca. However, individual shell Mg/Ca often results in unrealistic temperate estimates. The Sr/Ca ratios are relatively constant among the four species. Ratios of Mn/Ca and Ba/Ca are highest in G. menardii and are not reflective of elemental concentrations in open waters. The Mn/Ca ratio is elevated in all species during upwelling conditions, and a similar trend is demonstrated in Neogloboquadrina incompta shells from the California margin collected during upwelling periods. Together this suggests that elevated shell Mn/Ca may act as a tracer for upwelling of deeper water masses. Our results emphasize the large degree of trace element variability present among and within species living within a limited depth habitat and the roles of biology, calcification environment, and physical mixing in mediating how trace element geochemistry reflects environmental variability in the surface ocean.