We investigated the influence of hydrodynamic forcing (waves, tides, alongshore currents and winds) and net calcification by coral reef organisms on the spatial distribution of total alkalinity (TA) in a fringing reef system through a combination of field measurements and numerical modeling. A field experiment was conducted over 10 days in Coral Bay (Ningaloo Reef, Western Australia) during which we measured wave heights, currents, and tides as well as the spatial distribution of TA across the fore reef, reef crest, and lagoon. We used observed changes in TA on the adjacent reef flat, along with synoptic measurements of cross-reef transport, to estimate in situ rates of net calcification (g(cv)) using a control volume approach. Based on the g(cv) estimated, we simulated light-driven, diurnal variations in benthic net calcification within a three-dimensional ocean circulation model, ROMS (Regional Ocean Modeling System). By coupling ROMS with a spectral wave model (Simulating Waves Nearshore), we were able to simulate currents within Coral Bay reef-lagoon system that were in good agreement with the field observations and demonstrate that circulation with the system was wave-dominated. Both the field measurements and numerical model output confirmed that both residence time (tau(R)) and TA varied primarily with offshore wave heights and location within the bay. However, variations in TA were also affected by the nonlinear interaction between rates of net calcification that varied as a function of diurnally changing light and water residence time that varied as a function of offshore wave heights.