Dynamics of a seasonally low-inflow estuary: Circulation and dispersion in Elkhorn Slough, California

Elkhorn Slough is a small estuary---11 km long, 1 km wide, 4 m deep---along the Monterey Bay coastline, in central California. Pressured by development and severely impacted by agricultural run-off, Elkhorn Slough is a microcosm for studying how estuaries function as a buffer at the land/sea interface. To that end, it is essential to synthesize estuarine physics to a system scale, because the biogeochemical processes that occur within an estuary are ultimately dependent upon the residence time of water. This work develops a comprehensive picture of how different temporal and spatial scale physical processes contribute to circulation and dispersion in Elkhorn Slough. Fundamentally, the physics of Elkhorn Slough are applicable to short estuaries in general, as well as tidal creek networks that border larger systems such as San Francisco Bay.;Observations of current profiles were made continuously at two locations within the main channel of Elkhorn Slough for three and a half years. These long-term data sets reveal new insights into both tidal and seasonal circulation dynamics. Tides in Elkhorn Slough are mixed semi-diurnal, and are ebb dominant. Contrary to the typical association of tidal asymmetry arising from frictional forces in the momentum balance, roughly half of the ebb dominance in this system is shown to be due purely to the phase difference between the principal diurnal and semi-diurnal tidal constituents. This asymmetry is reinforced by the growth of overtides along the main channel. The propagation of the tide is a diffusion-like phenomenon, and each tidal constituent was observed to have its own wave speed due to frequency-dependent bottom drag. Residual circulation in upper Elkhorn Slough is a combination of barotropic and baroclinic mechanisms. Winter baroclinic circulation is complementary to the barotropic mechanisms, while the summer baroclinic circulation counteracts the barotropic motions. Elkhorn Slough is a low-inflow estuary during the summer months, and evaporation is significant enough to cause a reversal of the longitudinal density gradient. Inverse estuarine circulation was observed during the summer months, with residual surface currents in the channel directed landward and near-bed residual currents directed seaward; this is the opposite of classic estuarine circulation. The inverse estuarine density gradient was comparatively weak, however, and modal analyses of current structure, both in the main channel and on the shoal, indicate that the observed vertical exchange flows in the summer were predominantly due to lateral advection of slow moving water from the shoal to the channel on ebb.;Analysis of salt flux processes conducted with the numerical model TRIM3D revealed that the dominant longitudinal dispersion process is due to lateral trapping of water in the tidal creeks, however, the different dispersion mechanisms were found to be spatially and temporally variable, and to depend largely on local bathymetry. This dependence on local bathymetric variability largely precludes the application of a gradient dispersion coefficient that can be applied in a predictive manner at the system-wide scale. Dispersion rates in Elkhorn Slough are O(101 m2 s-1).;Curvature of the main charnel in Elkhorn Slough is a ubiquitous local bathymetric feature, and so a two-week field experiment was conducted to examine stratified and unstratified curvature-generated lateral circulation and momentum balances. In both stratified and well-mixed conditions, downstream adjustment of lateral circulation (non-linear advective acceleration) is of leading order in the lateral momentum budget; the depth-averaged term adjusts the streamline direction, while vertical deviations from the depth-average account for changes in lateral circulation. The asymmetry of forcing mechanisms on flood and ebb, due to variations in stratification and strength of tidal flow, can strongly affect net lateral transport and generation of residual currents in regions of curvature. Curvature increases longitudinal dispersion in well-mixed conditions, but not in stratified conditions, primarily because the presence of stratification inhibits vertical mixing.;The results of both the residual circulation observations and the salt flux analysis indicate that flushing time of upper Elkhorn Slough is approximately 5-12 days, depending on the spring-neap cycle and the magnitude of freshwater discharge to the head of the slough.