The transverse structure in the current and salinity distributions across the mouth of Delaware Bay are examined over the tidal and subtidal time scales. Results show that the across-estuary variation in bathymetry, in the form of a channel-shoal configuration, has a very significant impact on the characteristics of transverse variability. The mean current over the channel is characterized by a strong outflow of low salinity water in the upper layer and a strong inflow of high salinity water in the lower layer, consistent with the density-induced gravitational circulation. The mean flow pattern in the shallow waters over the shoals is marked by transverse rather than vertical variation. The subtidal current and salinity fluctuations are primarily driven by the effect of local atmospheric forcing. The subtidal current fluctuations in the upper layer of the channel are frictionally coupled to the local wind, resulting in downwind currents. The subtidal current fluctuations in the lower layer of the channel, however, flow in the direction of local setup and against the wind. With a wind blowing down the estuary, the wind-induced current tends to reinforce the two-layer structure of the gravitational circulation and substantially enhance the vertical shear and surface to bottom salinity difference. The reverse occurs with a wind in the up-bay direction. The subtidal currents in the shallow areas to the right of the channel exhibit largely depth-independent response to the effect of local wind, with downwind currents at both the surface and the bottom. At tidal frequencies the currents show only a modest variation across the bay mouth. Tidal currents are highly deterministic, but the characteristics of the tidal variability in salinity exhibit significant changes over long time scales. These long-term changes in the intratidal salinity variability are caused by the nonlinear interactions between the tidal and subtidal motions. The residual salt flux through the bay mouth shows significant subtidal fluctuations. The leading factor responsible for producing such subtidal fluctuations is the advection of salt by the wind-induced subtidal currents, but the effect of tidal pumping also contributes significantly to the overall residual salt flux into the estuary.