An important goal of coral reef ecology is elucidating the factors driving the distribution of corals, and to this end much attention has focused on disturbances and biotic agents. In this study, small-scale variations in the abiotic characteristics of seawater along the south coast of St. John, U.S. Virgin Islands, were quantified with the objective of assessing its potential to contribute to variation in coral community structure. This goal was achieved by combining several studies that were completed between 1994 and 2005, and were designed separately to measure flow, in situ light intensities, and dissolved inorganic carbon (DIC) chemistry. Together, the results reveal a slow westward surface flow at mean speed of 3.4 cm s^-1, and high residency times within semi-enclosed bays. Upstream versus downstream locations periodically differed in light levels, and short-term measurements of DIC chemistry identified diel variation in aragonite saturation state that appeared to intensify in downstream locations. The association between flow and the abiotic properties of seawater suggests that small-scale patterns in water circulation are related to physical gradients that have the potential to mediate the distribution of corals.