Water movement through the framework of Davies Reef, a coral reef in the central Australian Great Barrier Reef, was studied using field and laboratory determinations of permeability, tide gauge measurements of water levels, dye tracers, and pore water chemistry. Flow is driven by current, wind-induced, or tide-induced water level differences which were shown to occur between reef front and lagoon. The reef is hydraulically very heterogeneous with bulk flow occurring through high permeability zones (voids and rubble) at a velocity on the order of 10 m/d. Pore water exchange in less permeable zones occurs at a much slower rate. Vertical components of flow are significant. Chemical data indicate that carbonate precipitation and solution occur so that porosities, permeabilities, and flow paths may change with time. Implications for nutrient transfer through the benthic sediments and for fresh water resources on reef islands are discussed.