Bed-sediment grain-size and morphologic data from Suisun, Grizzly, and Honker Bays, CA, 1998-2002

The USGS Place Based Studies Program for San Francisco Bay investigates this sensitive estuarine system to aid in resource management. As part of the inter-disciplinary research program, the USGS collected side-scan sonar data and bed-sediment samples from north San Francisco Bay to characterize bed-sediment texture and investigate temporal trends in sedimentation. The study area is located in central California and consists of Suisun Bay, and Grizzly and Honker Bays, sub-embayments of Suisun Bay. During the study (1998-2002), the USGS collected three side-scan sonar data sets and approximately 300 sediment samples. The side-scan data revealed predominantly fine-grained material on the bayfloor. We also mapped five different bottom types from the data set, categorized as featureless, furrows, sand waves, machine-made, and miscellaneous. We performed detailed grain-size and statistical analyses on the sediment samples. Overall, we found that grain size ranged from clay to fine sand, with the coarsest material in the channels and finer material located in the shallow bays. Grain-size analyses revealed high spatial variability in size distributions in the channel areas. In contrast, the shallow regions exhibited low spatial variability and consistent sediment size over time. Introduction The San Francisco Bay estuary begins at the confluence of the Sacramento and San Joaquin Rivers in central California. Since the discovery of gold in 1848, the region has undergone immense environmental changes. Hydraulic mining activity during the late 1800’s in the Sierra Nevada resulted in the influx of large quantities of sediment to the San Francisco Bay estuary (Gilbert, 1917; Cappiella et al., 1999). At the same time, increased development has resulted in the loss of wetlands, re-routing of rivers, and species decline. The USGS Place Based Studies Program is an inter-disciplinary program aimed at understanding the San Francisco Bay estuary system, its response to modern stresses, and disseminating information to aid in resource management of the area. As part of the San Francisco Place Based Studies Program, the USGS began research in northern San Francisco Bay to characterize bed-sediment texture and investigate temporal trends in sedimentation. The study area comprises approximately 170 km and consists of Suisun Bay, and Grizzly and Honker Bays, sub-embayments of Suisun Bay (Fig. 1). At present, the region is characterized by three channels. The primary navigation channel is situated on the south side of Honker Bay into Suisun Bay, where it passes south of Ryer Island. A smaller channel runs between Roe Island and Ryer Island. The third channel flows through Suisun Cutoff, north of Ryer Island, on the south side of Grizzly Bay, and through the Reserve Fleet Channel on the western side of Suisun Bay. All three channels join at Carquinez Strait where they continue through the southern section of San Pablo Bay and into the Central Bay. The channels and shallows range in depth from 10 to 22 m and 1 to 2 m, respectively. During the years 1998 through 2002, the USGS collected bed-sediment samples, and performed three side-scan sonar surveys of the region. We completed grain-size and statistical analyses on the sediment samples, which were compiled in a spreadsheet and are included with this report as Tables 2 and 3. The side-scan sonar data (Plate 1) from one survey was digitally mosaiced and interpreted to reveal bed morphology and composition. Methods The following section describes sample collection, sediment grain-size analyses, and side-scan sonar data collection. Sediment Sample Collection Sediment sampling took place between December 1998 and January 2002 using two USGS research vessels, the RV David Johnston and the RV Polaris. Table 1 summarizes the details regarding each cruise such as the research vessel, cruise ID, cruise dates, the number of samples collected, and whether side-scan sonar data was collected. Additional information on these cruises can be found at the link provided in Table 1. The goal of the sampling scheme with the RV Johnston was to collect samples before and after the rainy season to investigate possible seasonal changes in bed texture (Table 1). The sample locations using this vessel are displayed on Figures 2-5 with symbols colored to represent percent sand-sized material. Percent sand is emphasized in this report as a means of characterizing the bimodal distribution of grain sizes in the samples. The sediment sampling locations ranged from Montezuma and Suisun Sloughs to the north, Honker Bay to the east, and Carquinez Strait to the west. Sampling was largely concentrated in the channel area known as Garnet Sill (Fig. 1; Plate 1) due to its location as an important area of estuarine mixing adjacent to the large shallow-water habitat of Grizzly Bay (Schoellhamer, 2001). Sampling depths ranged from 1.17 m to 15.63 m. Table 1: Sediment sample and side-scan data collection Vessel Cruise ID/Information Cruise Date Number of Samples SideScan Sonar RV David Johnston J-5-98-SF http://walrus.wr.usgs.gov/infobank/j/j598sf/html/j5-98-sf.fmeta.outline.html December 1-2, 1998 28 Yes RV David Johnston J-2-99-SF http://walrus.wr.usgs.gov/infobank/j/j299sf/html/j2-99-sf.fmeta.outline.html March 48, 1999 56 Yes RV David Johnston J-3-99-SF http://walrus.wr.usgs.gov/infobank/j/j399sf/html/j3-99-sf.fmeta.outline.html November 15-18, 1999 85 Yes RV David Johnston J-1-00-SF http://walrus.wr.usgs.gov/infobank/j/j100sf/html/j1-00-sf.fmeta.outline.html March 1315, 2000 64 No RV Polaris P-1-00-SF http://walrus.wr.usgs.gov/infobank/p/p100sf/html/p1-00-sf.fmeta.outline.html August 89, 2000 11 No RV Polaris P-2-00-SF http://walrus.wr.usgs.gov/infobank/p/p200sf/html/p2-00-sf.fmeta.outline.html November 7-8, 2000 12 No RV Polaris P-1-01-SF http://walrus.wr.usgs.gov/infobank/p/p101sf/html/p1-01-sf.fmeta.outline.html February 6-7, 2001 7 No RV Polaris P-2-01-SF http://walrus.wr.usgs.gov/infobank/p/p201sf/html/p2-01-sf.fmeta.outline.html February 26-27, 2001 12 No RV Polaris P-3-01-SF http://walrus.wr.usgs.gov/infobank/p/p301sf/html/p3-01-sf.fmeta.outline.html June 1920, 2001 12 No RV Polaris P-4-01-SF http://walrus.wr.usgs.gov/infobank/p/p401sf/html/p4-01-sf.fmeta.outline.html October 16-17, 2001 12 No RV Polaris P-1-02-SF http://walrus.wr.usgs.gov/infobank/p/p102sf/html/p1-02-sf.fmeta.outline.html January 22-23, 2002 12 No The RV Polaris was used for seven sampling cruises from 2000 to 2002 as indicated on Table 1. Unlike the Johnston cruises, samples were collected at 12 specific sites (Fig. 6) at variable intervals throughout the year. These locations are part of a network of long-term monitoring sites used by the USGS (see http://sfbay.wr.usgs.gov/access/wqdata/ for more information). Sampling depths ranged from 1.5 m at locations 415, 416, and 417, to 17.4 m at location 8.1 (Fig. 6). The shallow regions in the sloughs and Grizzly Bay were sampled using a smaller boat transported aboard the RV Polaris. We used two types of equipment for the sampling: a Van Veen grab sampler, and box cores. The grab sampler has a clam-like scoop, and can penetrate about 20 cm deep. Sampling involved careful selection of the surface layer of sediment (top ~1 cm) into two sample bags, one for archive and one for analysis. The majority of the RV Johnston samples and all of the RV Polaris samples were collected using this instrument. A few samples on the RV Johnston cruise were collected by scraping the fine surface sediment from the top of a box core. Occasionally, samples were taken from various intervals below the surface in the grab or core. The specific equipment and interval used for each sample is indicated on Tables 2 and 3. After collection, samples were stored in a refrigerator on board the boat, and then transferred to a refrigerator in Menlo Park where they were stored at 3.8 C. Sediment Grain-Size Analysis Grain-size analysis typically lasted about one week for a batch of 30 samples. All instrumentation used for the analysis is located on the USGS Menlo Park campus. The following sections describe the various instruments used and a detailed account of the laboratory procedures. Differing Grain-Size-Analysis Methodologies Comparisons between the RV Johnston datasets are hampered by the changing methodologies used for the grain-size analysis. We used three different methods of analysis on the RV Johnston samples during the course of the project. The oldest samples of the data set (J-5-98-SF) were processed using the Rapid Sediment Analyzer (RSA) for the intermediates, and the Micromeritics 5100 Sedigraph for the fine material. 10 samples from the J-2-99-SF cruise were analyzed using the RSA for the intermediates, and the Coulter LS100Q laser particle-size analyzer for the fines. The remaining RV Johnston samples and all of the RV Polaris samples were processed utilizing only the laser particle-size analyzer for both size fractions. It is important to note that the RV Polaris samples were processed by the same individual and used a consistent analysis method, facilitating comparisons between samples throughout the study period. The techniques used to analyze the samples from the RV Johnston and the RV Polaris are indicated on Tables 2 and 3, respectively. The changing methodologies were due to the limitations of the Sedigraph in processing the finest fraction (<0.0005 mm) of material. As a result, the data for the J-5-98-SF cruise show an increase in this size fraction as seen on Figures 7A and B. The laser particle-size analyzer was ultimately chosen as the best laboratory technique because of its ability to analyze a large range of grain sizes (0.0003 mm to 1.0 mm, 11.5 phi to 0 phi,), resulting in the use of only one instrument. In order to facilitate comparisons between the samples, we omitted the coarsest material (>1 mm) from the RV Johnston samples for the computer analysis. We made this change for two reasons: 1) this size