Record-High Specific Conductance and Water Temperature in Bay during Water Year 2015 The San Francisco estuary is commonly defined to include (bay) and the adjacent Sacramento– Delta (delta). The U.S. Geological Survey (USGS) has operated a high-frequency (15-minute sampling interval) water-quality monitoring network in San Francisco Bay since the late 1980s (Buchanan and others, 2014). This network includes 19 stations at which sustained measurements have been made in the bay; currently, 8 stations are in operation (fig. 1). All eight stations are equipped with specific conductance (which can be related to salinity) and water-temperature sensors. Water quality in the bay constantly changes as ocean tides force seawater in and out of the bay, and river inflows—the most significant coming from the delta—vary on time scales ranging from those associated with storms to multiyear droughts. This monitoring network was designed to observe and characterize some of these changes in the bay across space and over time. The data demonstrate a high degree of variability in both specific conductance and temperature at time scales from tidal to annual and also reveal longer-term changes that are likely to influence overall environmental health in the bay.

In water year (WY) 2015 (October 1, 2014, through September 30, 2015), as in the preceding water year (Downing-Kunz and others, 2015), the high-frequency measurements revealed record-high values of specific conductance and water temperature at several stations during a period of reduced freshwater inflow from the delta and other tributaries because of persistent, severe drought conditions in .This report briefly summarizes observations for WY 2015 and compares them to previous years that had different levels of freshwater inflow.

Instrumentation and Data Collection At each monitoring station, YSI Inc. Model 6920 V2 water-quality sondes are deployed on a taut cable mount at a constant elevation above the bottom of the bay; thus, the water depth above the sensors varies as tides rise and fall. At some stations, sensors are located at two different elevations above the bottom to reveal vertical variations (fig. 2). Data from monitoring stations are telemetered using a cellular modem and uploaded daily to USGS database servers. Telemetry facilitates rapid and remote evaluation of sensor performance and scheduling of field maintenance to minimize data gaps. Sensor output is affected by biological growth, which usually increases with time and requires the affected data to be edited or deleted; other periods of missing data are caused by instrument failures or construction projects near monitoring stations (Wagner and others, 2006). The scope of the dataset is shown in table 1; all data are archived as provisional in near-real time in the USGS National Water Information System (http://waterdata.usgs.gov/nwis) and undergo review 122°30' 122°15' 122° before final approval. Further details on methods are available at P e ta R l http://ca.water.usgs.gov/projects/baydelta/. iv u e m N r a a p a R Benicia iv e SAN PABLO r Bridge BAY Carquinez Bridge Sacramento– 38° San Joaquin Delta Instrument Richmond/San Rafael Bridge shelter

CENTRAL San Francisco Bay SAN FRANCISCO BAY C Davit Alcatraz A L I Island F O R Bay N Sensor cable Bridge Pier 17 Bridge I A

37°45' Suspension Sensor SOUTH line head SAN FRANCISCO BAY Sensor carriage

OCEAN EXPLANATION (not to scale) San Mateo Continuous water-quality monitoring site Mid-depth sensor Bridge and carriage Dumbarton Near-bottom sensor PACIFIC Bridge 37°30' and carriage Weight

Alviso Slough 0 5 10 MILES 0 5 10 KILOMETERS (Schematic not to scale)

Figure 1. Locations of fixed water-quality monitoring stations in San Francisco Figure 2. Typical monitoring-station installation. Bay, California, for the 2015 water year (October 1, 2014, to September 30, 2015).

U.S. Department of the Interior ISSN 2331-1258 (online) Open-File Report 2017–1022 U.S. Geological Survey https://doi.org/10.3133/ofr20171022

sac15-0579_fig 02

Sac15-579_fig 01 The high-frequency monitoring network produced instantaneous Water Year 2015 Records measurements at 15-minute intervals, measuring water temperature and specific conductance 96 times per day, or 35,040 times per year. During WY 2015, the monitoring network recorded instantaneous Annual maximum values and annual mean values for specific values of specific conductance and water temperature at several stations conductance and water temperature were computed for each station that exceeded all previous values in the period of record. Between water and compared to results from previous years. To ensure that annual years 2014 and 2015, every station in the network saw a new record mean values were representative despite periods of missing data, the for one or both of these parameters. Record-high values for specific following thresholds were applied: if more than 33 percent of the data conductance were measured in WY 2015 at Benicia Bridge, Carquinez for a given water year were missing or if the duration of any one gap Bridge, Dumbarton Bridge, and Alviso Slough (fig. 3). Record-high was longer than 45 consecutive days, the mean value for that water water temperatures in WY 2015 were measured at Carquinez Bridge, year at that site was not computed. Annual mean values were also Richmond/San Rafael Bridge, , Pier 17, San Mateo excluded for stations that had periods of record of less than 5 years Bridge, and Dumbarton Bridge (fig. 4). (Dumbarton Bridge and Pier 17, table 1). Salinity was computed according to the Practical Salinity Scale 1978 (Fofonoff and Millard, 1983) from measured specific conductance; values are unitless. Annual Mean Values and Relation to Freshwater Drought conditions in the region affect water quality in the Inflow bay by reducing freshwater inflow from the watershed. To study Annual mean values of specific conductance and water temperature the effects of differences in freshwater inflows and to compare varied spatially within the bay (fig. 5). The Alcatraz Island station (fig. 1) WY 2015 values to those from previous years, we used annual freshwater inflow volume from the delta, which was estimated with is closest to the Golden Gate, which is the ocean boundary of the San the DAYFLOW model (California Department of Water Resources, Francisco estuary. As noted, the Sacramento–San Joaquin River Delta, http://www.water.ca.gov/dayflow/). Output from this model includes to the northeast, serves as the major source of freshwater to the estuary the daily rate of freshwater flow from the delta to the bay, from which (fig. 1). From the ocean boundary toward the delta, specific conductance we calculated the annual volume of freshwater inflow from the delta. generally decreased (fig. 1, fig.A 5 ), whereas water temperature generally The annual volume of inflow from the delta is affected by hydrologic increased (fig. B5 ). Specific conductance in the southern part of the bay conditions and management actions but is generally smaller during (San Mateo Bridge, fig. 1) was similar to that near the ocean boundary drought conditions and, thus, provides context for the severity of the (Alcatraz Island station, fig. A5 ), but water temperature was warmer drought and its effect on water quality in the bay. than at the ocean boundary (fig. B5 ). This was due, in part, to relatively little freshwater inflow from the adjacent watershed and to the relatively Table 1. Water-quality monitoring stations included in this report, listed from

north to south. 122°30' 122°15' 122° N P a e p t a [U and L refer to the upper and lower sensor elevations in the water column, respectively, R a

l R iv u

e m i v at stations equipped with two instruments. Station water depths are reported relative to r a

e mean lower low water] r Benicia U: 43,400 Oct. 9, 2014 Bridge L: 44,700 Aug. 29, 2015, Sept. 3, 2015 Sensor SAN PABLO SUISUN BAY Water Year BAY elevation U:38,700 July 31, 2015 Station name and number depth, above monitoring 38° Carquinez L: 40,100 Oct. 14, 2014 in meters bottom, began Bridge in meters U: 49,300 Aug. 29, 2008 EXPLANATION L: 50,100 July 12, 2014 Richmond/ Continuous specific-conductance Suisun Bay at Benicia Bridge 24 23 U 2001 San Rafael Bridge monitoring sites 11455780 7.6 L CENTRAL U: Upper sensor record-high SAN FRANCISCO Alcatraz value and date at 24 15 U 1999 BAY Island L: Lower sensor record-high Carquinez Bridge1 11455820 1.8 L 51,000 June 14, 2004 Bay value and date San Francisco Bay at 14 9.1 U 2006 Bridge Red: Record-high value, and date Golden Gate (record was set in WY 2015) Richmond/San Rafael Bridge 1.5 L Bridge Pier 17 49,900 July 8, 9, 11, 13, 2014 375607122264701 37°45' San Francisco Bay at 4.9 3.0 2003 San Francisco Bay Alcatraz Island SOUTH San SAN FRANCISCO 374938122251801 Francisco BAY San Francisco Bay at Pier 17 8.5 1.2 2013 Los Angeles OCEAN 374811122235001 U: 51,100 Sept. 9, 2014 L: 51,300 Sept. 20, 21, 23, 24, 25, 26, 2014 San Francisco Bay at San Mateo 15 13 U 1990 3.0 L Bridge near Foster City 11162765 San Mateo Dumbarton Bridge South San Francisco Bay at Bridge 14 7.6 U 2011 PACIFIC 37°30' Dumbarton Bridge2 Alviso Slough 1.2 L 0 5 10 MILES U: 51,900 Sept. 22, 2015 373015122071000 L: 52,200 Sept. 22, 2015 0 5 10 KILOMETERS Alviso Slough near Alviso 1.0 0.5 2010 48,700 Sept. 12, 13, 2015 11169750 1Station temporarily discontinued during bridge construction June 10, 2012–April 23, 2014. Figure 3. Maximum (record-high) instantaneous specific conductance from all 2Station temporarily discontinued during bridge construction October 1, 2011–March 16, 2013. data at each site sensor. Measured in microsiemens per centimeter.

sac15-0579_fig3 122°30' 122°15' 122° shallow water depths in the southern part of the bay. Variability in annual

P N e a volume of freshwater inflow from the delta over the preceding 25 years ta p R l a iv u e m R r a was high (fig. 5C). Total volume of inflow from the delta in WY 2015 iv e r Benicia was only slightly higher than the WY 2014 value, revealing continued U: 23.0 July 24, 25, 26, 2006Bridge SAN PABLO L: 22.8 Aug. 16, 2015 SUISUN BAY drought conditions. BAY Of the six stations with sufficient WY 2015 data to compute annual U:24.5 June 22, 2006; July 21, 26, 2006 38° Carquinez L: 24.0 July 24, 25, 26, 2006 means, record-high annual mean specific conductance and water- Bridge U: 21.9 Aug. 17, 2015 EXPLANATION temperature values were recorded at two (fig. A5 ) and five (fig. 5B) L: 21.1 Aug. 16–17, 2015 Richmond/ Continuous water-temperature of the stations, respectively. Variability in annual mean specific San Rafael Bridge monitoring sites CENTRAL U: Upper sensor record-high conductance can be partially attributed to variability in the annual SAN FRANCISCO Alcatraz value and date volume of freshwater inflow from the delta (fig. 6), which affects BAY Island L: Lower sensor record-high flushing rates across the bay (Walters and others, 1985). For all stations, 20.1 July 26, 2014; Aug. 28, 2015 Bay Bridge value and date Red: Record-high value, and date annual mean specific conductance and the annual volume of inflow Golden Gate (record was set in WY 2015) from the delta were inversely related, such that lower inflow volumes Bridge Pier 17 20.4 Aug. 29, 2015 were associated with greater annual mean specific conductance values 37°45' San Francisco Bay (fig. 6). Stations farthest from the major source of freshwater inflow (Alcatraz Island, Richmond Bridge, and San Mateo Bridge; fig. 1) SOUTH San SAN FRANCISCO Francisco converged to nearly equivalent, high, mean specific conductance values BAY during years with the lowest inflow volumes, indicating that the bay is Los Angeles OCEAN more influenced by inflow of coastal ocean waters during drought, when U: 24.0 Aug. 30, 2004; Sept. 9, 10, 2004; July 25, 26, 27, 2006; Aug. 7, 2015 L: 23.9 July 27, 2014 freshwater inflows from the delta are low. San Mateo Dumbarton In the past decade, the 2 years featuring the greatest annual inflow Bridge Bridge from the delta (2006 and 2011) coincided with clear reductions in annual

PACIFIC 37°30' mean specific conductance in the bay (fig.A 5 ). In WY 2015, the increase 0 5 10 MILES U:25.3 July 26, 2014 Alviso Slough L:25.4 Aug. 16, 2015 in inflow from the delta, compared to the previous year, was very slight, 0 5 10 KILOMETERS 27.1 June 30, 2013 and most sites saw annual mean values of specific conductance that were similar to the previous year. Annual mean water temperatures, however, Figure 4. Maximum (record-high) instantaneous water temperature from all data again increased notably in WY 2015. Changes in annual mean ocean at each site sensor. Measured in degrees Celsius. seawater or air temperature could both have contributed to this trend.

x104 A 5 33 For reference, specific conductances

4 26 of 5,000 and 50,000 microsiemens per centimeter (µS/cm) at 25 degrees EXPLANATION 3 Benicia 19 Celsius (°C) are equivalent Carquinez to salinities of 2.7 and 32.7, Richmond 2 12

Alcatraz Mean salinity (-) respectively. Specific conductance San Mateo Alviso and salinity of freshwater are both

Mean specific conductance, 1 6

in microsiemens per centimeter near 0; coastal ocean water has B 20 a specific conductance of about 52,000 µS/cm at 25 °C and a salinity 18 of about 34.

16 Figure 5. Annual mean values from 14 1990 to 2015. Where two sensors were in degrees Celsius available, the upper sensor is shown: A, Mean water temperature, 12 annual mean specific conductance and x1010 C salinity, by station; B, annual mean water 6 temperature, by station; and C, annual volume of freshwater inflow from the 4 Sacramento–San Joaquin River Delta (delta) to the San Francisco Bay, based 2 on DAYFLOW model output. Years with in cubic meters

Inflow from delta, insufficient data were excluded (for example, Carquinez Bridge during water 0 1990 1995 2000 2005 2010 2015 years 2012–14). Diamonds indicate the Water year most recent (water year 2015) data.

sac15-0579_fig04

Sac15-0579_fig 05 x104 The Alviso Slough specific conductivity dataset 5 33 is shorter in length, but the data appear to be somewhat anomalous when plotted against delta inflow (fig. 6). This site is located near several heavily managed former salt 4.5 29 ponds, and management activities can affect annual mean salinities independently of drought impacts, for example, if 4 26 the outflow volume of salt pond water is sufficiently large compared to the receiving body. The temperature time series, however, displays a trend consistent with the other 3.5 22 sites (fig. B5 ). Water temperature and salinity (computed from 3 19 observed water temperature and specific conductivity) are important to human and ecological issues in the bay (see 2.5 15

Shellenbarger and Schoellhamer, 2011) and elsewhere. Annual mean salinity (-) These two water-quality parameters impact aquatic habitats and can affect the distribution and abundance of aquatic 2 12 vegetation and organisms in the bay. Only consistent long-term monitoring data can reveal trends resulting from 1.5 9 changing hydrologic conditions and management actions and from responses to disturbances, such as the severe Annual mean specific conductance, in microsiemens per centimeter 1 6 California drought that began in 2012. 0 1 2 3 4 5 6 7 Annual volume inflow from delta, in cubic meters x1010 References Cited EXPLANATION Benicia Alcatraz Buchanan, P.A., Downing-Kunz, M.A., Schoellhamer, Carquinez San Mateo Richmond Alviso D.H., Shellenbarger, G.G., and Weidich, K.W., 2014, Continuous water-quality and suspended-sediment Figure 6. Annual means of specific conductance (left axis) and salinity (right axis) at each transport monitoring in the San Francisco Bay, California, station as a function of annual volume of freshwater inflow from the Sacramento–San Joaquin water years 2011–13: U.S. Geological Survey Fact Sheet River Delta (delta) to the San Francisco Bay. For stations with two sensors (table 1), only the 2014–3090, 4 p., https://dx.doi.org/10.3133/fs20143090. upper sensor is shown. Diamonds indicate the most recent (water year 2015) data. Downing-Kunz, M.A., Work, P.A., and Shellenbarger, G.G., 2015, Record-high specific conductance and Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, B.A., 2006, temperature in San Francisco Bay during water year Guidelines and standard procedures for continuous water-quality monitors— 2014 (ver. 1.1, December 28, 2015): U.S. Geological Station operation, record computation, and data reporting: U.S. Geological Survey Open-File Report 2015–1213, 4 p., accessed at Survey Techniques and Methods 1–D3, 51 p., 8 attachments, accessed at http://pubs.usgs.gov/of/2015/1213/ofr20151213.pdf. http://pubs.water.usgs.gov/tm1d3. Fofonoff, N.P., and Millard, R.C., 1983, Algorithms for Walters, R.A., Cheng, R.T., and Conomos, T.J., 1985, Time scales of circulation computation of fundamental properties of seawater: and mixing processes in San Francisco Bay waters: Hydrobiologia, v. 129, no. 1, UNESCO Technical Papers in Marine Science, v. 44, p. p. 13–36. 6–9. Suggested Citation Shellenbarger, G.G., and Schoellhamer, D.H., 2011, Continuous salinity and temperature data from San Work, P.A., Downing-Kunz, M.A., and Livsey, D., 2017, Record-high specific Francisco Estuary, 1982–2002—Trends and salinity- conductance and water temperature in San Francisco Bay during water freshwater inflow relationship: Journal of Coastal year 2015: U.S. Geological Survey Open-File Report 2017–1022, 4 p., Research, v. 27, no. 6, p. 1191–1201. https://doi.org/10.3133/ofr20171022.

Acknowledgments For Additional Information Collection of these data was supported by the U.S. Army Visit: http://ca.water.usgs.gov/projects/baydelta/ Corps of Engineers, San Francisco District, as part of the Regional Contact: Monitoring and Regional Sediment Management Programs; Paul A. Work at [email protected], Interagency Ecological Program; California State Coastal Maureen A. Downing-Kunz at [email protected], Conservancy; Bureau of Reclamation; U.S. Geological Survey— or Daniel Livsey at [email protected]. San Francisco Bay Pilot Study for the National Water Quality U.S. Geological Survey Monitoring Network for U.S. Coastal Waters and their Tributaries; California Water Science Center U.S. Geological Survey—Priority Ecosystems Science Program; and 6000 J Street, Placer Hall the U.S. Geological Survey Federal/State Cooperative Program. Sac15-0579_fig 06Sacramento, CA 95819