Cuttings recovered from two deep exploratory wells in the Lihue Basin, Kauai, Hawaii, include fossiliferous marine deposits that offer an uncommon opportunity to study paleoenvironments from the deep subsurface in Hawaii and interpret the paleogeography and geologic history of Kauai. These deposits indicate that two marine incursions gave rise to protected shallow-water, low-energy embayments in the southern part of the Lihue Basin in the late Pliocene–early Pleistocene. During the first marine incursion, the embayment was initially zoned, with a variable-salinity environment nearshore and a normal-marine reef environment offshore. The offshore reef environment eventually evolved to a nearshore, variable-salinity environment as the outer part of the embayment shallowed. During the second marine incursion, the embayment had normal-marine to hypersaline conditions, which constitute a significant departure from the variable-salinity environment present during the first marine incursion. Large streams draining the southern Lihue Basin are a likely source of the freshwater that caused the salinity fluctuations evident in the fossils from the first marine incursion. Subsequent volcanic eruptions produced lava flows that buried the embayment and probably diverted much of the stream flow in the southern Lihue Basin northward, to its present point of discharge north of Kalepa Ridge. As a result, the embayment that formed during the second marine incursion received less freshwater, and a normal-marine to hypersaline environment developed. The shallow-water marine deposits, currently buried between 86 m and 185 m below present sea level, have implications for regional tectonics and global eustasy.