To better understand how the hydrology of bar-built estuaries affects breaching and closing patterns, a model is developed that incorporates an estuary hydrologic budget with a geomorphic model of the inlet system. Erosion of the inlet is caused by inlet flow, whereas the only morphologic effect of waves is the deposition of sand into the inlet. When calibrated, the model is able to reproduce the initial seasonal breaching, seasonal closure, intermittent closures and breaches, and the low-streamflow (closed state) estuary hydrology of the Carmel Lagoon, located in Central California. Model performance was tested against three separate years of water-level observations. When open during these years, the inlet was visually observed to drain directly across the beach berm, in accordance with model assumptions. The calibrated model predicts the observed 48-h estuary stage amplitude with root mean square errors of 0.45m, 0.39m and 0.42m for the three separate years. For the calibrated model, the probability that the estuary inlet is closed decreases exponentially with increasing inflow (streamflow plus wave overtopping), decreasing 10-fold in probability as mean daily inflow increases from 0.2 to 1.0m3/s. Seasonal patterns of inlet state reflect the seasonal pattern of streamflow, though wave overtopping may become the main hydrologic flux during low streamflow conditions, infrequently causing short-lived breaches. In a series of sensitivity analyses it is seen that the status of the inlet and storage of water are sensitive to factors that control the storage, transmission, and inflow of water. By varying individual components of the berm system and estuary storage, the amount of the time the estuary is open may increase by 57%, or decrease by 44%, compared to the amount of time the estuary is open during calibrated model conditions for the 18.2-year model period. The individual components tested are: berm height, width, length, and hydraulic conductivity; estuary hypsometry (storage to stage relationship); two factors that control wave-swash sedimentation of the inlet; and sea level rise. The elevation of the berm determines the volume of water that must enter the estuary in order to breach, and it modulates the wave-overtopping flux and frequency. By increasing estuary storage capacity, the estuary will breach less frequently (−27% change in time open for modeled excavation scenario) and store water up to 3months later into the summer. Altering beach aquifer hydraulic conductivity affects inlet state, and patterns of breaching and water storage. As a result of sea-level rise of 1.67m by 2100, and a beach berm that remains in its current location and accretes vertically, the amount of time the estuary remains open may decrease by 44%. Such a change is an end-member of likely scenarios given that the berm will translate landwards. Model results indicate that the amount of time the estuary is open is more sensitive to changes in wave run-up than the amount of sand deposited in the inlet per each overtopping wave.