Graham's Harbor is a 2 x 3 km, windward, high-energy lagoon located at the northeast end of San Salvador. It is open to the west and rimmed to the north and east by cays and a barrier reef. Today this lagoon contains areas of rippled and bioturbated sand as well as areas of sparse to dense seagrass. Sediment probes and bathymetric surveys indicate that Graham's Harbor was an irregular, bowl-shaped basin that now contains up to 4 m of sediment and water depths to 6 m. Thirty-nine surface samples and 5 sediment cores have been evaluated with respect to texture, composition, and mud fraction mineralogy. An additional 9 cores were examined megascopically. Cluster analysis of 111 samples and 10 variables reveals four marine facies in Graham's Harbor: 1) grapestone, 2) abraded grain "grain/packstone," 3) Halimeda -rich "packstone," and 4) grapestone-rich "pack/wackestone." These facies are distributed vertically and laterally in a well-defined, non-random pattern within the lagoon and reflect control of deposition by benthic communities and modification by transport resulting from waves and currents. Three surficial facies are found in the lagoon: grapestone, abraded grain "grain/packstone," and Halimeda -rich "packstone." The primary controls of lateral distribution of these facies are benthic flora and energy of waves and currents. Water depth does not appear to influence lateral Facies distribution in Graham's Harbor. The grapestone facies blankets most of the lagoon today, where the substrate is not stabilized by benthic flora and is exposed to intermittent wave and current energy. Rimming the lagoon on the east and north is the abraded grain "grain/packstone" facies. This facies accumulates along the barrier reef and next to the northern cays, areas which receive more continuous wave energy. Halimeda -rich "packstone" is found only in a protected (lower wave energy) area of the lagoon that has been stabilized by seagrass. The grapestone-rich "pack/wackestone" is not found in the surficial sediments of Graham's Harbor. Studies of sediment cores reveal a coarsening-upwards sedimentary sequence. Grapestone-rich "pack/wackestone" (sandy mud) is overlain by the grapestone facies (sand). The sequence is capped by abraded grain "grain/packstone" (muddy sand). The sedimentary sequence in Graham's Harbor suggests initial deposition within a silled basin comprised of lower energy, normal marine, muddy sediments (grapestone-rich "pack/wackestone"). Aggregates in this facies were probably transported from the west during storms. As sea-level rose above the sill, less muddy, higher energy sediments (grapestone and abraded grain "grain/packstone") were deposited. Radiocarbon dates of peat and sediment from cores indicate that the entire carbonate sequence formed in less than 7,000 years at rates of 27-95 cm/1,000 years.