A two-dimensional, two-channel, laterally averaged estuarine circulation model (LAECIM) with a sigma coordinate in the vertical is developed for tides, tidal currents, and salinity in a two-channel estuary with any arbitrary angle. The model is forced by oceanic tides composed of 16 major constituents and freshwater discharge. The two channels are governed by the same dynamic equations. A control volume at the junction between the two channels is designed to conserve mass and volume transport and to guarantee the continuity of momentum in the finite difference schemes, based on the physical principle in continuum medium of fluid. An explicit leapfrog scheme in time and centered differencing in space are employed, together with a time filter to remove the computational mode. An Euler backward scheme is periodically used to correct (retard) the phase frequency, which is overestimated due to the explicit leapfrog scheme used. The model is applied to the entire San Francisco Bay with its two channels: the main north-south channel and the Golden Gate channel, which is perpendicular to the former (i.e., with a right angle to the former). The simulated time series of tides, tidal currents, and salinities compare favorably with the observed tidal gauge data and moored current and salinity time series during the summer 1980. The simulated along-channel salinity section also compares well to the conductivity-temperature-depth sectional observations during the same period. The model simulated Eulerian residual current is consistent with two-layer flow theory. ¿ 1998 American Geophysical Union