Quarterly Progress Reports for Sedimentation in the Delta and Suisun Bay
The following reports are edited to present interesting developments in the project operations.
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Listing of each task (by title) and percentage complete:
Delta site installation -- 90%
Suspended-sediment data collection in the Delta -- starting
Suspended-sediment data collection in Suisun Bay -- continuing
Design database format for riverbed elevations -- done
Measure bedform profiles in lower Sacramento River -- continuing
Measure bedform profiles in lower San Joaquin River -- continuing
Measure bedform profiles in Three Mile Slough -- continuing
Create HTML document to present riverbed monitoring -- 10%
Completion of milestones/tasks/deliverables (status):
Design and build portable system for bedform monitoring -- completed
Implement GPS mapper to use as navigational aid for boat captains -- completed
Write a data report -- not started
Data analysis -- continuing
Write an interpretive report -- not started
Description of any contract or task order amendments or modifications:
USGS sediment transport researchers in Colorado would like to use our data on the lower San Joaquin River to help them develop numericial sediment transport models at no cost to CALFED. Grids were surveyed in the lower San Joaquin above Three Mile Slough. The location of large bars and the orientation of sand dunes indicate that sediment may move up the San Joaquin River some distance during tidal cycles after delivery from Three Mile Slough. The data collected for bedform transport and sediment flux can be used to develop a model and to examine movement of sediment from Three Mile Slough up the San Joaquin River. The results will be provided to CALFED.
Problems encountered:
The riverbeds are more dynamic than theorized. More detailed profile grids will be obtained to follow changes in bedforms through tidal cycles and storm flows.
Data recorders store the output from the suspended-solids concentration sensors installed at the study sites. New programs for the data recorders have been tested and are being revised due to an unexpected conflict with ultrasonic velocity meters (UVMs) located at some of the sites in the Delta.
Description of benefits/objectives of project achieved:
The data collected to date show that sand waves are ubiquitous, that the riverbeds are subject to several meters of scour and fill in response to storm flows, and that bedload can indeed be estimated from bedform movement.
Listing of each task (by title) and percentage complete:
Delta site installation -- 100%
Suspended-sediment data collection in the Delta -- 20%
Suspended-sediment data collection in Suisun Bay -- 20%
Design database format for riverbed elevations -- done
Measure bedform profiles in lower Sacramento River -- 20%
Measure bedform profiles in lower San Joaquin River -- 20%
Measure bedform profiles in Three Mile Slough -- 20%
Create HTML document to present riverbed monitoring -- 50%
Completion of milestones/tasks/deliverables:
Suspended load measurement -- Operation of sites at Freeport, Rio Vista, Three Mile Slough, Stockton, and Jersey Point continued. Equipment to measure depth, velocity, salinity, temperature, and SSC through the wet season was deployed in Cache Slough on November 17. The first wet season pulses from the Central Valley watershed occurred during the quarter. Initial review of data indicates that two sediment pulses passed Freeport during higher flows in late November and early December.
Bed load measurement -- Hydrographic surveys were made in the San Joaquin River on November 24 and December 2. 24 channel cross sections for river modeling over a 5 mile reach were obtained in one day. Bed load movement surveys were made on the Sacramento River above Haycock Shoals on December 11 and 18. Hardware improvements were obtained for the sonar which reduced the time for data processing of bathymetric data. A video camera housing and imaging card were purchased to allow for streambed observation.
Write a data report -- not started
Data analysis --
Two sediment pulses came down the Sacramento River in late November and early December and pretty much dissipated in the Delta. OBS time series show riverine pulses at Freeport and Suisun Bay sediment resuspended by wind-waves. The attached figure shows discharge at Freeport and OBS millivolts at Freeport, Rio Vista, Threemile Slough, and Mallard Island (near-surface sensor). These sensors have not been calibrated yet, but a rule of thumb is to multiply by 0.3 to get SSC in mg/L. Flow at Vernalis went up only a few hundred cfs and the Stockton OBS was somewhat fouled but did not show any flow relation. These data and analyses are very preliminary (and subject to revision) but indicate the episodic nature of sediment transport this time of year.
Freeport flow: Increased from 20000 cfs to 60000 cfs slowly and sometimes in steps from mid November to mid December.
Freeport OBS: Two well-defined peaks occur in late November and early December. The first peak is a little bigger and occurs when discharge goes from about 30-40 K and the second peak is when discharge goes from 40-60 K. These peaks occur about 3 days after rainfall in the watershed. The duration of each peak is only about 2 days.
Rio Vista OBS: The OBS was fouling but it still shows increases about 1-2 days after the peaks at Freeport, which indicate the arrival of the Freeport peaks at Rio Vista.
Threemile OBS: The SSC peaks in Threemile slough are from the pulses coming down the Sacramento River. Tidal variations increase in late November and again in early December as the peaks arrive. There is also a general tidally-averaged trend of increasing SSC followed by decreasing SSC that is probably caused by resuspension associated with a spring tide.
Mallard Island OBS: Generally similar to Threemile Slough. The single tidally-averaged hump at Mallard seems to lead that at the slough. Tidal variation increases seemingly a little faster than at Threemile Slough. With closer examination, the tidal peaks at Mallard appear to be wind-wave generated in Suisun Bay as they appear at the start of flood tide. There were some very strong winds during this time. The peaks are also at Mallard on Nov 26-27 but not at the slough. So the time series at Mallard appears to be more influenced by wind-wave resuspension in Suisun Bay and less by the riverine pulses observed at Freeport. The spring tide in early December also increases SSC.
Streambed profile grids on Sacramento River above Haycock Shoals were compared for August and December 1998. Bed elevation was lower in December by about 1 meter throughout the channel. Sand bedforms that were prevalent in August were not evident in December. Instead, sonar readings indicated a coarse bed of gravel or larger material. The December grids were measured during a period of high discharge partly caused by reservoir releases. A tentative explanation for the lowering of bed elevation and disappearance of sand bedforms is that the underlying material is too coarse for transport. Further surveys are planned to determine the extent of the bed lowering and to document the nature of the bed material.
The hydrographic survey of the San Joaquin River from Three Mile Slough to the marina above Seven Mile Slough was completed in two days. Twenty-four cross sections and 4 longitudinal profiles were obtained. Cross-section data were conformed to straight line projections. The topography shown in nautical maps of the reach was consistent with the new survey. Additional deposition was especially apparent at the west end of Santa Clara shoals. The topographic channel data will be used to model flow and sediment transport numerically.
Longitudinal profiles for December 1998 in the San Joaquin River above Three Mile Slough showed the presence of sand bedforms migrating upriver. The same configuration of bedforms was documented in June 1998. Velocity records at nearby USGS gaging stations confirm that water flows from Three Mile Slough to the San Joaquin River during flood tides, which would promote sediment transport upriver. Further surveys are planned to determine the upriver extent of sediment transport.
Write an interpretive report -- The primary interpretive report has not been started. An abstract and poster about the project will be presented at the State-of-the-Estuary meeting in March 1999. The abstract is attached.
Description of any contract or task order amendments or modifications: none
Problems encountered: No major problems.
Description of benefits/objectives of project achieved:
The data collected to date show that sand waves are ubiquitous, that the riverbeds are subject to several meters of scour and fill in response to storm flows, and that bedload can indeed be estimated from bedform movement. Suspended load has not yet been calculated, pending analysis of water samples and calibration of optical sensors. The qualitative character of the sensor output, however, indicates that suspended-solids concentration in the Delta is less variable than in the Bay during summer.
Continuous data collected during the first flush in November and December 1998 indicate that sediment transport is episodic with pulses dissipating within days. The transition from riverine to estuarine dominance is also apparent within the Delta. Riverine pulses, spring tides, local resuspension, and wind-wave resuspension in Suisun Bay are all factors affecting suspended sediment transport.
Listing of each task (by title) and percentage complete:
Delta site installation -- 100%
Suspended-sediment data collection in the Delta -- 33%
Suspended-sediment data collection in Suisun Bay -- 33%
Design database format for riverbed elevations -- done
Measure bedform profiles in lower Sacramento River -- 33%
Measure bedform profiles in lower San Joaquin River -- 33%
Measure bedform profiles in Three Mile Slough -- 33%
Create HTML document to present riverbed monitoring -- 50%
Completion of milestones/tasks/deliverables:
Suspended load measurement -- Operation of sites at Freeport, Rio Vista, Three Mile Slough, Stockton, and Jersey Point continued. Equipment to measure depth, velocity, salinity, temperature, and SSC through the wet season was recovered and redeployed in Cache Slough in mid November. A small sediment pulse was observed at the Delta sites in late January and a larger sediment pulse was observed in the Delta and Mallard Island in mid-February. Extra samples were collected during these pulses.
Bed load measurement -- The streambed of the Sacramento River was surveyed at low, medium, and high flow during the quarter. An inexpensive video system for observing bed material at depths up to 45 feet was devised and tested. Bed material was recorded in the Sacramento River below Garcia Bend and at Three Mile Slough. A longitudinal profile of the Sacramento River was surveyed from Hood to Garcia Bend on January 19, 1999. The profile consisted of straight segments along alternating sides of the channel to minimize bias and maximize the length of profile. The lines were recorded as GPS lat-long positions separated by about 1 meter. The surveyed lines will be revisited in the next quarter to assess changes in bedforms and bars at various scales following high flows. Three Mile Slough and a section of the San Joaquin River were surveyed on March 26, 1999.
Video camera for bed material: A video camera was inserted in a portable housing that can be lowered to the streambed by hand. The housing is weighted with outrigger lead. While the boat drifts at river velocity, the housing is suspended by garden hose, through which power and video cables are strung. A DC-powered TV/VCR is operated on the boat to record views of the bed material as the face of the housing contacts the bed. Bed material is visible even in turbid water. The lens and camera can reproduce the mint year on a dime, so sand grains and pebbles are easily visualized.
Bedforms and bars are displayed in river surveys with sonar, but bed material cannot be judged accurately from the survey profiles. Bed material can be sampled with bedload or grab samplers, but the operation is labor intensive, produces high lab costs, and the resulting data have minimal use except where hydraulic conditions are measured thoroughly. However, knowledge of whether the bed material is sand, gravel, or cohesive clay is essential to interpretation of sediment movement. The use of an inexpensive video system to obtain information about bed material is an effective substitute, and has been used concurrently with sonar profiling surveys.
Related point: coarse sand was visible throughout the channel center in the Sacramento River, with occasional views of fine gravel and unidentified clams. Coarse sand was visible throughout the slough center in Three Mile Slough, where the sand bed is also rippled. In Three Mile Slough, flocculated sediment marked the lee-side of ripples, and was suspended slightly by the passage of local turbulence.
Write a data report -- not started
Data analysis --
The velocity record from Cache Slough had some gaps but showed that flow switched from bidirectional to unidirectional in mid-February when the Yolo Bypass began to flow. At Freeport, SSC was less in February than during previous pulses. Throughout the western Delta, however, SSC was much greater in mid-February than during the previous pulses. The primary difference in mid-February was that the Yolo Bypass was flooded for the first time this winter.
While the flow into the Yolo Bypass is measured, the flow out of the Yolo Bypass is not measured, which makes it difficult to determine the effect of the Yolo Bypass on water quality of the Delta. Cache Slough may be a good place to measure the discharge of the Yolo Bypass because flow is unidirectional (from the Bypass when flowing) and the different source waters that create lateral banding in the Bypass seen by Ted Sommer and the Yolo Bypass PWT may be better or well mixed in Cache Slough.
Although previous surveys of the Sacramento River suggested that sand was scoured from the bed, the recent surveys showed that low-relief bedforms of sand were present at all stages. Therefore, sand was transported through the river to the Delta at all stages without obvious depletion.
Analysis of the Three Mile Slough profiles confirm the idea proposed in 1998, that sandy sediment from the Sacramento River enters Three Mile Slough during high flow and is transported to the south and up the San Joaquin River.
Three surveys at Sacramento River below Garcia Bend: The sampling grid at Sacramento River below Garcia Bend was surveyed on January 19, February 2, and March 12, 1999. After the survey on February 2, a trend in bedform regime was apparent. At flows below 40,000 cfs, the bedforms are well-defined with recognizable dune profiles. Above 40,000 cfs, the bed displays only low-relief bedforms that lie long the minimum elevation of dune troughs. The sand in the Sacramento River is not depleted at high flow; instead, it is transported rapidly at higher concentrations in the water column to the Delta. As flow recedes, the sand settles to the bed and forms recognizable dunes again. Two related points: high flows move sand rapidly from the Sacramento River to the Delta, but high flows were not observed to deplete sand from the river channel. Sand delivery from upstream has not apparently been eliminated by reservoirs.
Sampling grid in San Joaquin River above Three Mile Slough: To assess whether previous surveys over the shoal above Three Mile Slough had detected a common transport condition, a detailed grid was planned and surveyed on March 26, 1999. The transition between eastward and westward movement of dunes past the shoal was mapped. Two surveys and a sampling grid indicate that the shoal preserves the appearance of eastward-migrating dunes. Therefore, sand from the Sacramento River appears to supply sediment to the shoal above Three Mile Slough, and may transport sand as far as Santa Clara Shoal. Related point: this assessment of sand deposition has been made to provide background for agencies proposing to use sediment from these shoals for rehabilitation projects.
Write an interpretive report -- The primary interpretive report has not been started. An abstract and poster about the project were presented at the State-of-the-Estuary meeting in March 1999.
Description of any contract or task order amendments or modifications: none
Problems encountered: The Benicia Bridge monitoring site has been out of service longer than expected due to seismic retrofit work on the Bridge.
Description of benefits/objectives of project achieved:
The data collected to date show that sand waves are ubiquitous, that the riverbeds are subject to several meters of scour and fill in response to storm flows, and that bedload can indeed be estimated from bedform movement. Suspended load has not yet been calculated, pending analysis of water samples and calibration of optical sensors. The qualitative character of the sensor output, however, indicates that suspended-solids concentration in the Delta is less variable than in the Bay during summer.
Continuous data collected during the first flush in November and December 1998 indicate that sediment transport is episodic with pulses dissipating within days. The transition from riverine to estuarine dominance is also apparent within the Delta. Riverine pulses, spring tides, local resuspension, and wind-wave resuspension in Suisun Bay are all factors affecting suspended sediment transport. The first flush of the Yolo Bypass may be a large source of sediment to the western Delta and the Yolo Bypass alters the hydrodynamics of Cache Slough.
Listing of each task (by title) and percentage complete:
Delta site installation -- 100%
Suspended-sediment data collection in the Delta --40%
Suspended-sediment data collection in Suisun Bay -- 40%
Design database format for riverbed elevations -- done
Measure bedform profiles in lower Sacramento River -- 40%
Measure bedform profiles in lower San Joaquin River -- 40%
Measure bedform profiles in Three Mile Slough -- 40%
Create HTML document to present riverbed monitoring -- 50%
Completion of milestones/tasks/deliverables:
Suspended load measurement -- Operation of sites at Freeport, Rio Vista, Three Mile Slough, Stockton, and Jersey Point continued. The near-surface sensor at Mallard Island failed and was replaced. Sensor calibration data for the Delta sites were reviewed and the calibrations were found to be acceptable but more high concentration samples will be needed. Our Delta sampling scheme was adjusted to sample every 2 months during the dry season and every 2 weeks during the wet season. Instruments that measure velocity, water depth, conductivity, temperature, and SSC in Cache Slough were recovered in early April and repositioned in Delta Smelt spawning grounds in the Slough as part of an IEP-sponsored study. The instruments will be recovered in early July.
Bed load measurement -- The following streambed surveys were conducted during the quarter:
Sacramento River at Garcia Bend: April 29 and May 6. Sacramento River from Rio Vista to Decker Island: May 25-26. Three Mile Slough: April 19. San Joaquin River from Three Mile Slough to Jersey Point, including cross sections: April 19-20.
Economical three-dimensional plotting software for riverbed data was obtained and used to show bedform orientation to survey grids, triangulate grids, derive surface contours of depositional reaches, and to compute bedform migration rates. An underwater video housing was refined and used to observe streambed composition directly from a boat.
The project was reviewed by the USGS Office of Surface Water in April. Favorable comments and some helpful suggestions were received.
Write a data report -- not started
Data analysis -- continuing, see above.
Write an interpretive report -- The primary interpretive report has not been started. Randal Dinehart has drafted an article for the ASCE Journal of Hydraulic Engineering entitled 'Sand bedload measured by single-beam surveys in estuarine rivers' that describes methods and initial results of the project.
Description of any contract or task order amendments or modifications: none
Problems encountered: The Benicia Bridge monitoring site has been out of service longer than expected due to seismic retrofit work on the Bridge.
Description of benefits/objectives of project achieved:
The data collected to date show that sand waves are ubiquitous, that the riverbeds are subject to several meters of scour and fill in response to storm flows, and that bedload can indeed be estimated from bedform movement. Suspended load has not yet been calculated, pending final analysis of water samples and calibration of optical sensors. Preliminary sensor calibration data for the Delta sites were reviewed in spring 1999 and the calibrations were found to be acceptable but more high concentration samples will be needed. The qualitative character of the sensor output, however, indicates that suspended-solids concentration in the Delta is less variable than in the Bay during summer.
Continuous data collected during the first flush in November and December 1998 indicate that sediment transport is episodic with pulses dissipating within days. The transition from riverine to estuarine dominance is also apparent within the Delta. Riverine pulses, spring tides, local resuspension, and wind-wave resuspension in Suisun Bay are all factors affecting suspended sediment transport. The first flush of the Yolo Bypass may be a large source of sediment to the western Delta and the Yolo Bypass alters the hydrodynamics of Cache Slough.
Project publications:
Dinehart, R.L., and Schoellhamer, D.H., 1999, Sedimentation in the Delta of the Sacramento and San Joaquin Rivers: Proceedings of the 4th biennial State of the Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 75.
Oltmann, R.N., Schoellhamer, D.H., and Dinehart, R.L., 1999, Sediment inflow to the Sacramento-San Joaquin Delta and the San Francisco Bay: Interagency Ecological Program newsletter, v. 12, no. 1, pp. 30-33
Listing of each task (by title) and percentage complete:
Delta site installation -- 100%
Suspended-sediment data collection in the Delta --55%
Suspended-sediment data collection in Suisun Bay -- 55% Design database format for riverbed elevations -- done
Measure bedform profiles in lower Sacramento River -- 55%
Measure bedform profiles in lower San Joaquin River -- 55%
Measure bedform profiles in Three Mile Slough -- 55%
Create HTML document to present riverbed monitoring -- 50%
Completion of milestones/tasks/deliverables:
Suspended load measurement -- Operation of sites at Freeport, Rio Vista, Three Mile Slough, Stockton, and Jersey Point continued. An autosampler was used at Mallard Island to collect calibration samples for a new near-surface sensor. In early July, equipment deployed in Cache Slough as part of an IEP sponsored study of Delta Smelt habitat was recovered. Unfortunately, the current meter did not operate properly. OBS, conductance, and temperature instruments gave good results. David Schoellhamer talked with Carl Chen about sediment transport and sediment oxygen demand in the San Joaquin River near Stockton.
Bed load measurement --
Constructed new mount to array 4 transducers across bow of boats. Improved synchronization of sensor times to 0.2 sec with software to increase positional accuracy of measured depths. The 3-D plotting program Tecplot was found to provide a better method for deriving bedform profiles from irregular survey data than the existing method of point projection. Equivalent profiles are cross-correlated to measure rates of bedform migration.
Sacramento River below Garcia Bend: The bedform grid below Garcia Bend was surveyed five times during July and August (July 16, 20, 27, August 6, 12). Bedload transport rates were calculated for the 4 intervals between surveys. Bedload transport rates correlated well with continuous velocity records at the gaging station 4 miles downstream, Sacramento River at Freeport. The transport-velocity line was also consistent with the higher transport rate measured in August 1998. Results indicate that measurements over a range of flows could be made to develop a bedload rating, if needed.
A longitudinal profile was measured on Aug. 6 from Garcia Bend to Freeport to assess patterns of seasonal sediment movement. Profile features were compared with previous surveys in Oct. 1997, July 1998, and Jan. 1999.
Three Mile Slough: An expanded, detailed grid was prepared for the 1-km reach near the gaging station, which was surveyed on Sept. 13 and 29. Each survey required about 5 hours of boat time to complete. The resulting contour maps (attached) show the migration of sand throughout the area in the absence of significant riverine supply. Bedforms moved away from the San Joaquin at the west side of the slough, and moved toward the San Joaquin at the east side of the slough. The mapped movement confirmed previous hypotheses about sand transport between the Sacramento and San Joaquin Rivers.
With the 4-transducer method for bedform mapping tested successfully, it will be applied at other Delta sites where bedload sampling is not applicable. Probable survey areas include Old River and Cache Slough. Probable areas have been chosen near gaging stations to provide reference to water-surface elevation.
Write a data report -- The water year 1998 data report was sent to cooperator, colleague, and specialist review. The report contains SSC data from the Benicia Bridge and Mallard Island sites that are supported by this study and other Bay sites supported by the U.S. Army Corps of Engineers San Francisco District as part of the Regional Monitoring Program. Randal Dinehart and David Schoellhamer outlined a USGS Professional Paper that will present results from this study. The report will be a combined data and interpretive report.
Data analysis -- Data analyses of the bedform-transport surveys, longitudinal profile surveys, and suspended-load data will continue for preparation of a USGS report.
Write an interpretive report -- Randal Dinehart and David Schoellhamer outlined a USGS Professional Paper that will present results from this study. Randal Dinehart has drafted an article for the ASCE Journal of Hydraulic Engineering entitled 'Sand bedload measured by single-beam surveys in estuarine rivers' that describes methods and initial results of the project.
Description of any contract or task order amendments or modifications:
We would like to discuss project accomplishments and continuation of the project beyond September 2000 with CALFED staff.
We had initially expected to move instruments from Freeport to Dutch Slough this autumn. Because the Freeport instrument provides valuable data during high flows, we will keep operating the Freeport site this year and deploy other equipment at Dutch Slough.
We had initially expected to write a data report and an interpretive report for this project. Instead, data from SSC monitoring sites at Mallard Island and Benicia will be included in an annual series of data reports that include data from other Bay monitoring sites supported by the U.S. Army Corps of Engineers San Francisco District as part of the Regional Monitoring Program. Suspended and bed load data from the Delta will be included in a USGS Professional Paper that will include data interpretation.
Problems encountered:
The Benicia Bridge monitoring site has been out of service longer than expected due to seismic retrofit work on the Bridge.
Description of benefits/objectives of project achieved:
The data collected to date show that sand waves are ubiquitous, that the riverbeds are subject to several meters of scour and fill in response to storm flows, and that bedload can indeed be estimated from bedform movement. Suspended load has not yet been calculated, pending final analysis of water samples and calibration of optical sensors. Preliminary sensor calibration data for the Delta sites were reviewed in spring 1999 and the calibrations were found to be acceptable but more high concentration samples will be needed. The qualitative character of the sensor output, however, indicates that suspended-solids concentration in the Delta is less variable than in the Bay during summer.
Continuous data collected during the first flush in November and December 1998 indicate that sediment transport is episodic with pulses dissipating within days. The transition from riverine to estuarine dominance is also apparent within the Delta. Riverine pulses, spring tides, local resuspension, and wind-wave resuspension in Suisun Bay are all factors affecting suspended sediment transport. The first flush of the Yolo Bypass may be a large source of sediment to the western Delta and the Yolo Bypass alters the hydrodynamics of Cache Slough.
Project publications:
Dinehart, R.L., and Schoellhamer, D.H., 1999, Sedimentation in the Delta of the Sacramento and San Joaquin Rivers: Proceedings of the 4th biennial State of the Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 75.
Oltmann, R.N., Schoellhamer, D.H., and Dinehart, R.L., 1999, Sediment inflow to the Sacramento-San Joaquin Delta and the San Francisco Bay: Interagency Ecological Program newsletter, v. 12, no. 1, pp. 30-33
A list of additional publications by the USGS San Francisco Bay and Delta Sediment Transport Project is available at http://water.wr.usgs.gov/abstract/sfbay/sfbaycontbib.html