Sanctuary Integrated Monitoring Network
Monitoring Project

Hydrodynamics and sedimentation in Elkhorn Slough

Principal Investigator(s)

  • Stephen Monismith
    Stanford University
  • Adina Paytan
    Stanford University


  • SIMoN
Start Date: September 01, 2002
End Date: December 30, 2005

The goal of this project has been to develop a detailed understanding of the hydrodynamics and sediment dynamics of Elkhorn Slough through a combination of numerical modeling, hydrographic field measurements, and tracer chemistry.
The hydrographic field work we discuss in this report is primarily based on two 3 week
long experiments, one carried out in September 2002, the other performed in April 2003.

During each experiment we deployed a variety of instruments for measuring currents, water levels, and temperatures at a series of 5 stations arrayed along the length of the Slough. More limited measurements of salinity were made during the 2002 experiment.

Summary to Date

The major results of the field work are:

(1) Water levels in the Slough are nearly in-phase – i.e., the water surface in the Slough moves up and down in response to tides in Monterey Bay as though it were a flat surface. As a result, tidal currents are proportional to the rate of change in sea-surface elevation, enabling first-order predictions of currents to be made using predicted water level variations.

(2) Currents below Parsons Slough are relatively constant in strength, partially reflecting the fact that much of the tidal prism of the system is upstream of the confluence of Parson’s Slough and the main stem of Elkhorn Slough. The decrease in cross-sectional area with distance from the Highway 1 Bridge also contributes to maintaining the strength of tidal currents below Parson’s Slough.

(3) Currents in Elkhorn Slough are ebb dominant – i.e., the shorter duration ebbs have stronger currents than are observed during floods. The likely effect of this on sediment transport is pronounced since bottom stresses, which drive erosion of sediments, are substantially larger on
ebbs than on floods. The net effect is a mean ocean-ward flux of sediments. This flux would appear to be strongly modulated by the fortnightly spring-neap cycle.

(4) Tidal excursions are a considerable fraction of the length of the Slough. As observed in measured temperatures and inferred from integration of current measurements, at spring tides, a water parcel that is located at Kirby Park at the end of the flood can travel nearly the entire length of the Slough on the following ebb. During neap tides, water motions are somewhat reduced.

(5) Flows in many sections of Elkhorn Slough are spatially complex. In most cross-sections, flows are stronger in the deepest section, although in Seal Bend, the region of maximum ebb current wanders from side to side through the bend. Immediately upstream of the Highway 1 Bridge, there are pronounced secondary flows on ebbs. These lead to predictable variations in acoustic backscatter intensity that suggest cross-sectional variations in the distribution of

(6) Bottom drag coefficients, “constants” that relate bottom stress to local velocity vary from the canonical value of 0.002 near Kirby Park to values as large as 0.0075 in the reach below Parson’s Slough.

Monitoring Trends

  • Temperature loggers show a strong longitudinal temperature gradient with low temperatures at the mouth (ca. 12 degrees C) reflecting Monterey Bay water, whereas at the head of the slough, temperatures reached as high as 23 degrees C reflecting heating of the slough by incident solar radiation.
  • Radium samples taken at low tide show a consistent increase in activity moving up the channel, except at one station (which was possibly not taken from within the channel). Moreover, the slightly elevated activity near the mouth suggests a possible source of water into the harbor from the Salinas River. Finally, samples taken at areas outside the Slough itself show high activities in side ponds, which suggests low mixing between ponds and the Slough proper.


Numerical modeling of currents and sediments was carried out using the 3D circulation model TRIM3D, a hydrodynamic model that has been applied to a number of estuarine systems like San Francisco Bay, the Venice Lagoon Tomales Bay, and the low salinity zone of the Saint Lawrence River. The 10 m resolution bathymetric grid was based on data provided by the CSUMB Seafloor mapping laboratory and extended from the Highway 1 Bridge to the head of the estuary. Lacking data for major portions of the intertidal zone of the Slough, bathymetry for much of the shallowest parts of the system were based solely on edges defined by USGS topographic maps. Flows in the model were forced by imposing observed variations in sea level at the downstream boundary, Driven by tides observed in September 2002, and using bottom friction coefficients (roughness lengths) that we have used in modeling other estuaries, the model did a good job of reproducing observed water levels, although, in light of the flat surface behavior, this is not a stringent test. Currents were reproduced with reasonable accuracy, although currents near Kirby Park were better predicted than were currents near the Highway 1 Bridge. This may reflect shortcomings in the bathymetry data, in particular, a general lack of data from the Parson’s Slough drainage. Increasing the model resolution was from 2 vertical layers to 7 layers improved the predicted velocities, although instabilities of the wetting front (the water’s edge during filling and emptying of the Slough) also emerged, suggesting that the treatment of wetting and drying in TRIM3D may need improvement for application to systems like Elkhorn Slough. A second limitation to the accuracy of current predictions is the effect of fixed resolution of the grid relative to the size of smaller channels and features in the slough, which are not well represented by 10 m grid.

The hydrodynamic code was supplemented by a sediment “module” previously used to predict cohesive sediment behavior in South San Francisco Bay. Using velocities calculated by the hydrodynamic code, this module computed the erosion, deposition and transport of sediments. Erosion and deposition were calculated using standard models of these processes, models that entail specifying 4 empirical parameters related both the sediments themselves and to the state of the bed from which they are eroded.
The sediment model shows clearly that the Slough is erosional. When run with the same parameters used previously for South San Francisco Bay, most of the Slough showed net erosion although there were also significant regions of deposition. In contrast, observations of changes in Slough bathymetry show only erosion. This highlights the need to obtain specific measurements of the needed sediment parameters, including some limited assessment of their spatial variability.

Computation of residence time by computing the transport of tracers that initially mark selected regions of the Slough show that downstream of Parson Slough, the residence time is quite short, possibly less than 1 day, depending on when in the spring-neap cycle and even at what phase of the tide the tracer is introduced. In contrast, upstream of Kirby Park, the residence time was appeared to be greater than the length of time the calculation was run (ca. 14 days). Work with the hydrodynamic/sediment model is ongoing as part of LOBO (Land Ocean Biogeochemical Observatory, an NSF funded project lead by Ken Johnson of MBARI), and current efforts are focused on developing a new grid based on new bathymetric data (also from CSUMB) which includes LIDAR surveys of the intertidal zone. The new grid will also include Moss Landing Harbor and may extend into Monterey Bay so as to enable study of ocean-estuary exchange.
Measurement of four Radium isotopes (223Ra, 224Ra, 226Ra, and 228Ra) made at 5 stations along the length of the Slough show that there may be significant groundwater inputs to Elkhorn Slough, with computed flows varying from 5 to 50 m3/s depending on the time of year and the isotope used to compute the flow. Averaging over all the Radium data, the groundwater flow we computed was 34 ± 29 m3/s.

The picture these observations make is that while details of flows in Elkhorn Slough may be complex, overall, it is clear that because of its ebb dominance, Elkhorn Slough is currently exporting sediment to Monterey Bay. The fact that the water levels in the Slough are more or less the same as in Monterey Bay and change little along the length of the Slough also suggests that any measure, e.g. sills (P. Williams 1992), aimed at muting tides in the Slough would either need to be of a length along the channel that is comparable to the wavelength of the tides, or would need to impose hydraulically critically conditions at the sill or contraction to regulate water levels in the Slough. In any case, the current hydrodynamic/sediment model could be used to assess the qualitative, order of magnitude response to engineered features like sills, although details of the predictions could not be made with any confidence at the present time.

Study Parameters

  • Habitat
  • Sedimentation
  • Erosion
  • Turbidity

Figures and Images

Figure 1. Deployment of hydrographic instruments in Elkhorn Slough.

Figure 2. Typical instrument mooring design for an Acoustic Doppler Current Profiler (ADCP). This instrument is used to measure current velocities in the slough.

Figure 3. Temperature from Station 2 in April, 2003.

Figure 4. ADP frame used in the slough. Fine sediments on the bottom of the slough make it necessary to construct platforms that are stable and will not disappear into the mud.

Figure 5. An ADCP and its battery case.


  • Monismith et al. (2005)
    Hydrodynamics and sediment dynamics in Elkhorn Slough. A report to Monterey Bay Sanctuary Foundation.
    3.1 MB PDF