Caribbean biota underwent major ecological and evolutionary transformation in the Pliocene–Pleistocene, but a lack of detailed paleoenvironmental reconstruction prevents thorough resolution of cause and effect. We quantify levels of upwelling and freshwater input into Caribbean coastal shelf ecosystems over the last ∼6 m.y. with >3300 stable isotope measurements from 74 fossil serially sampled gastropods by normalizing δ18O values to open-ocean δ18O from planktonic foraminifera. We find that the influence of Pacific-like upwelling in the southwestern Caribbean was low after 4.25 Ma but coastal ecosystems were heavily influenced by seasonal freshening until ca. 2.5 Ma, after which time low-freshwater conditions were established. The origination of modern oligotrophic coastal conditions was therefore a result of oceanographic change causing declining upwelling, and declining nutrients from terrestrial sources. We speculate that a southward shift of the Intertropical Convergence Zone, associated with Northern Hemisphere glaciation, reduced rainfall and terrestrial nutrient input and contributed to biotic turnover in the southwestern Caribbean, including the proliferation of modern reef communities.