The salinity budget in an estuary is analyzed using an isohalline as the seaward bounding surface of the volume of integration. It is found that the rate of change of volume integrated salinity is governed by two processes: (1) the drift of the isohaline through the fluid, and (2) turbulent salt flux through the isohaline. This analysis highlights the role of turbulent salt flux in maintaining the salinity intrusion. In contrast, more standard budgets using a stationary, vertical cross section as the seaward end of the volume of integration attribute almost all along-estuary salt flux to advective processes such as the gravitational circulation. The isohaline budget is explored using an analytical model and using results from a three-dimensional numerical model. The numerical results highlight the complex spatial and temporal interplay between turbulent mixing and the shape of the isohaline. Averaging over a time period during which the freshwater volume behind the isohaline is constant reduces the isohaline budget to a balance of two terms: the time-mean, area-integrated turbulent salinity flux across the isohaline being equal to the mean river flow times the salinity of the isohaline. ¿ 2001 American Geophysical Union