To help define the habitat of modern marine stromatolites, wave-dominated flow and sediment transport were studied in the shallow subtidal region (1–2 m depth) along the slightly concave, windward face of Highborne Cay, Exuma, Bahamas – the only face of the cay that includes a population of stromatolites concentrated near the region of highest curvature of the beach. Wave energy impacting this island's most exposed beach was driven by local wind forcing which increases largely in response to the passage of atmospheric disturbances that typically affect the region for periods of a few days. Although some wave energy is almost always noted (maximum horizontal orbital speeds at the bottom are rarely <10 cm s−1), wave conditions remain comparatively calm until local winds increase above speeds of ≈3–4 m s−1 at which point maximum wave speeds rapidly increase to 50–80 cm s−1. Stromatolites, which are largely restricted to the shoreward side of a shallow platform reef, are sheltered by the reef beyond which wave speeds are one to four times higher (depending on tidal stage). Moreover, stromatolite populations are predominantly found along a region of this wave-exposed beach that experiences comparatively reduced wave energy because of the curved morphology of the island's face. Maximum wave speeds are 1.4 to 2 times higher along more northern sections of the beach just beyond the locus of stromatolite populations. A quantitative model of sediment transport was developed that accurately predicted accumulation of suspended sediment in sediment traps deployed in the shallow subtidal zone along this beach. This model, coupled with in situ wave records, indicates that gross rates of suspended sediment deposition should be two to three times higher northward of the main stromatolite populations. Regions of the beach containing stromatolites nevertheless should experience significant rates of gross suspended sediment deposition averaging 7–10 g cm−2 day−1 (≈4–6 cm day−1). Results suggest that one axis of the habitat of modern marine stromatolites may be defined by a comparatively narrow range of flow energy and sediment transport conditions.