Miocene sediments of the Caribbean Gatun and Chagres formations, Panama Canal basin, were deposited within an archipelagic strait that connected Caribbean and Pacific waters. Shallow-water (∼ 25 m) benthic foraminifera of the Gatun Formation have a strong Caribbean affinity, indicating that a significant interoceanic, biogeographic barrier had formed at ∼ 8 Ma. However, benthic foraminifera of the overlying Chagres Formation are bathyal and markedly Pacific in affinity, indicating that at ∼ 6 Ma, waters of the Panama isthmian strait deepened to ∼ 200–500 m and Pacific bathyal waters flowed into the Caribbean. The Chagres Formation crops out at the Caribbean entrance to the Panama Canal in a large wedge of cross-laminated sandstone and coquina. The cross-laminations and coarse grain size indicate high-energy currents atypical of bathyal settings. We infer that a jet of the Pacific North Equatorial Countercurrent–Equatorial Undercurrent passed through the Panama isthmian strait to deposit these sediments on the Caribbean side. This later entry of Pacific taxa into the Caribbean had no apparent effect on the subsequent composition of Caribbean faunas.