Based on swath bathymetry, two-dimensional, high-resolution seismic reflection profiles, and Ocean Drilling Program/Deep Sea Drilling Project (ODP/DSDP) data, we describe a seafloor honeycomb pattern and propose a model for its formation in Pliocene–Miocene carbonate deposited on the uneven oceanic basement of the Carnegie Ridge (offshore Ecuador). Hydrothermal fluids derived from the basement aquifer fractured and dissolved carbonate sediment, creating seafloor pits above basements highs. Fluids expelled along polygonal faults may have assisted the nucleation of seafloor depressions. At the Pliocene-Pleistocene boundary, strong bottom currents scoured previously damaged sediments, enlarging the initial depressions and producing the seafloor honeycomb pattern. This regional erosive episode was contemporaneous with the final closing of the Isthmus of Panama and the clogging of the Ecuador Trench by the subduction of the Carnegie Ridge, so that the honeycomb pattern may be viewed as a regional marker of these two geodynamic events.