The hydrodynamics of a shallow estuarine subembayment were investigated in Honker Bay, a subembayment of Suisun Bay in northern San Francisco Bay. The brackish salinities, estuarine turbidity zone, and extensive shallows of Suisun Bay provide an important and unique biological habitat in the San Francisco Bay estuary. The research had three goals: to characterize circulation and spatial variability in currents and salinity within Honker Bay; to estimate the degree of exchange and the dynamics of exchange between Honker Bay and adjoining channels; and to evaluate the influence of Honker Bay on hydrodynamics of Suisun Bay, and more generally the influence of side-embayments on estuarine flows.

Three types of field experiments were conducted. Drogue studies were carried out to characterize Lagrangian circulation and estimate residence time in Honker Bay. Time-series measurements of velocity, salinity, temperature, and depth were collected for two three-month periods, to analyze temporal variability on the tidal, tidally-averaged (residual), and seasonal time scales, and to calculate harmonic constants. Profiles of velocity and salinity were collected in transects across Snag Channel (which connects Honker Bay to Suisun Cutoff) over a tidal cycle, to investigate the influence of channel curvature on secondary circulation and on lateral variability in salt flux.

Results showed that the tidal excursion in Honker Bay has the same order of magnitude as the length of the embayment. Therefore the residence time of water and suspended matter is short, ranging from less than one phase of the tide to several tidal cycles. The short residence time reduces the likelihood of juvenile fishes remaining in the shallows. At the same time, the semi-enclosed configuration of Honker Bay makes it more isolated from the channel than a typical shoal, and allows differences in characteristics such as salinity to develop between Honker Bay and the Main Channel. In summer there is a persistent gradient in tidally-averaged salinities of about 0.5 ppt/km across Honker Bay. Honker Bay contributes to longitudinal dispersion in Suisun Bay because of the multiple discrete sites of connection with the channel.

Residual currents, water transport, and salt flux are all up-estuary throughout Honker Bay in summer. The up-estuary residual currents are produced by the orientation of Honker Bay relative to the Main Channel, which restricts inflow during ebb tides but not during floods, and by the phase lag in currents between Suisun Cutoff and the Main Channel. Water-surface elevation at the Golden Gate accounts for most of the variability in elevation in Suisun Bay, but wind stress and tidal energy are also important. One-dimensional modeling showed that the predominantly westerly winds of summer reduce stratification, gravitational circulation, and the up-estuary movement of salt by enhancing turbulent mixing at the surface.

Flows out of Honker Bay into Snag Channel are rapidly mixed with water from the channel by strong intermittent secondary circulation. Early in the ebb tide, a lateral baroclinic pressure gradient (caused by differential advection) produces clockwise secondary circulation, while later in the ebb, centrifugal acceleration due to channel curvature produces counter-clockwise secondary circulation. The strength of the secondary circulation indicates the importance of channel curvature to mixing in northern San Francisco Bay and the Delta.