Until late Eocene time, the Bahamas platform extended to the present Virgin Islands, as demonstrated by magnetic, gravity, and refraction data. This interpretation is confirmed by the presence of widespread outcrops of middle Cretaceous through early Pliocene shallow-water bank carbonates below 5,200 m depth in the trench. Crustal thickness beneath this bank is 18-25 km. Igneous and metamorphic rocks from the base of the trench's southern slope are chemically very different from subduction-zone rocks.

Waters of the carbonate bank (300 × 100 km in size) transgressed southward after early Eocene time. During late Eocene time, the bank's southern margin was near today's shoreline where down-to-the-north growth faults formed. Along the bank's northern margin, block faulting produced a graben above the site of the modern Puerto Rico Trench. During middle Eocene to early Pliocene time, shallow-water deposition extended from a position presently 5,200 m deep in the trench to central Puerto Rico, an exceptionally stable block at least 100 km wide.

During middle Eocene time, the Beata Ridge dextral shear cut the trench off north of Hispaniola. In early Pliocene time, the Mona Canyon dextral fault zone cut across the trench, and strong northward tilting commenced. The trench's present southern slope is mainly a dip slope, inclined about 5°. The Puerto Rico Outer Ridge formed by lateral and upward movements of mantle materials that withdrew from beneath the sinking trench. Petroleum prospects presently are limited to the Tertiary (4,000 m thick) and to a coastal zone 20-25 km wide (to 2,000 m water depth). Traps are mainly fault seals and stratigraphic pinch-outs.

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