This dataset contains avian survey observations across four tidal marsh areas around San Francisco Bay. Multiple surveys were conducted around both high and low tides during the winter of 2010/11. Each survey alternated between scan and focals. During scans, all observable birds were counted. During focals, the behavior of a single, randomly selected bird was observed. Water level data was collected concurrently at each site and is provided with the avian survey data.

We completed four distinct projects to collect baseline data at varying spatial and temporal scales. First, we used data from aerial photographic surveys conducted from 1989-2014 to investigate region-wide trends in the populations of Common Murres and Brandt’s Cormorants. We used 173 observations of Common Murre colony abundance at 14 colonies and 123 observations of Brandt’s Cormorant nest abundance at 10 colonies over the 26-year study period. Additionally, aerial photographic surveys conducted in 2014 were used to document location and abundance of Common Murre, Brandt’s Cormorant, and Double-crested Cormorant across the NCSR. Second, at a more localized scale, we monitored Common Murre reproduction, foraging effort, and diet in 2014 at Castle Rock National Wildlife Refuge using a robotic, remotely-controlled video recording system. Although this is only one of the seabird colonies in the NCSR, it the largest and served to inform our understanding of the mechanisms of population change across the region. Common Murre are very visible and thus ideal for monitoring fine scale patterns in reproduction and changing diet. We measured date of nest initiation, hatching success, fledging success, overall reproductive success, time allocation, provisioning rate, and diet composition via the video. Information gained from these surveys were combined with comparable data from 2007-2013 at Castle Rock to assess baseline condition and variability of these metrics over an 8-year period. Third, in 2014-2015 we conducted ground-based surveys of coastally breeding seabirds inside and outside of six MPAs to establish a framework for continued MPA monitoring. For this, we conducted intensive monitoring of six species likely to benefit from MPA establishment: Pigeon Guillemot, Brandt’s Cormorant, Pelagic Cormorant, Double-crested Cormorant, Western Gull, and Black Oystercatcher. We collected data on breeding population size, breeding productivity, foraging rates and rates of human-caused disturbance inside and outside of each MPA. We monitored productivity by following individual nests visible from land and calculated annual breeding productivity as number of fledglings produced per breeding pair. We monitored foraging from land-based observation points, recording all birds foraging within a 1 km radius of an observation point. We calculated foraging rates as number of birds foraging per hour of observation. We recorded all human-caused disturbances observed during any land-based survey and calculated disturbance rates as number of disturbances per hour of observation.

The dataset includes three separate excel spreadsheets which provides waterbird (and predator) observations within individual survey units during the May 2019 breeding waterbird survey of south San Francisco Bay (2019WaterbirdSurveyFullData.xlsx), the total number of American avocets, black-necked stilts, and Forster's terns within each pond unit surveyed during the May 2019 survey (2019WaterbirdSurveyPondModel.xlsx), and the annual total number of nests for American avocets, black-necked stilts, and Forster's terns in south San Francisco between 2005 and 2019 (SouthBayWaterbirdNests2005-2019.xlsx).

The dataset includes three separate excel spreadsheets which provides waterbird (and predator) observations within individual survey units during the May 2019 breeding waterbird survey of south San Francisco Bay (2019WaterbirdSurveyFullData.xlsx), the total number of American avocets, black-necked stilts, and Forster's terns within each pond unit surveyed during the May 2019 survey (2019WaterbirdSurveyPondModel.xlsx), and the annual total number of nests for American avocets, black-necked stilts, and Forster's terns in south San Francisco between 2005 and 2019 (SouthBayWaterbirdNests2005-2019.xlsx).

Fifty-one tidal marsh sites across five regions (sub-embayments) were surveyed in the Delta, Suisun Bay, San Pablo Bay, central San Francisco Bay, and South San Francisco Bay. Vegetation surveys spanned ten years, from July 2008 to January 2018. A total of 5,112 plots were surveyed. Plots were positioned on transects along an elevation gradient and evenly distributed across each site, where possible, to capture spatial variability along elevation and distance gradients. At each plot, percent cover of all plant species, bare ground, and litter as well as average height was visually assessed within a 0.25 m2 quadrat. Total plant cover in a plot could exceed 100 percent due to vegetation layering. Bare ground and litter cover was estimated as total area visible through the vegetation from above the plot. Vascular plant nomenclature followed Baldwin et al. (2012). Average plant height (in meters) was recorded at most sites. Geographic position (in UTM) and elevation (North American Vertical Datum of 1988, NAVD88) were recorded at each plot. Channel salinity was calculated at the site or multi-site scale (in PSU) with data from locally deployed water sensors or from San Francisco Bay National Estuarine Research Reserve (NERR) sites (Takekawa et al. 2013a, Thorne et al. 2019). All salinity values represent marsh channel or creek conditions, and not soil porewater salinity. A survey-grade Real Time Kinematic (RTK) global positioning systems (GPS) rover was used to measure location and elevation (plus or minus 1 cm horizontal, plus or minus 2 cm vertical manufacturer-stated accuracy; Leica Geosystems Inc., Norcross, Georgia). Rover positions were received in real time from the Leica Smartnet system using a CDMA modem (http://www.leica-geosystems.us/en/index.htm). The WGS 84 ellipsoid model was used for horizontal positioning and NAVD88 for vertical positioning. Rover accuracy and precision were evaluated by measuring positions at local National Geodetic Survey benchmarks; all errors were within the stated rover error. Elevation data was converted to z*, a unitless measure of elevation relative to the local tidal frame which accounts for variation in tidal range and allows for direct comparison across sites (Swanson et al. 2014). Local tidal datums were calculated from multiple sources including NOAA tide stations (https://tidesandcurrents.noaa.gov/), deployed water level loggers, and NOAA’s VDATUM model (Parker et al. 2003). Distance to channel was calculated as the distance (in meters) between each plot and the digitalized boundaries of all nearby channels and bays. Channels were digitized based on 2020 NAIP imagery supplemented with LiDAR when necessary. The centerline was digitized on small channels (appox. 1 - 2.5 m wide), while both edges were digitized on large channels (greater than 2.5 m), bays, and rivers. References Baldwin B. G., Goldman D. H., Keil D. J., Patterson R., Rosatti T. J. (2012). The Jepson manual: vascular plants of California. (Berkeley: University of California Press). Parker B., Milbert D., Hess K., Gill S. (2003). National VDatum–The implementation of a national vertical datum transformation database. Silver Spring: National Oceanic and Atmospheric Administration, National Ocean Service. 9. Swanson K. M., Drexler J. Z., Schoellhamer D. H., Thorne K. M., Casazza M. L., Overton C. T., et al. (2014). Wetland accretion rate model of ecosystem resilience (WARMER) and its application to habitat sustainability for endangered species in the San Francisco estuary. Estuaries Coasts 37, 476–492. doi: 10.1007/s12237-013-9694-0 Takekawa J. Y., Thorne K. M., Buffington K. J., Freeman C. M., Powelson K. W., Block G. (2013). Assessing marsh response from sea-level rise applying local site conditions: Humboldt Bay National Wildlife Refuge. Unpubl. Data Summary Report (Vallejo, CA: USGS Western Ecological Research Center). 44pp + Appendices. Thorne K. M., Backe K. E., Freeman C. M., Buffington K. J., Forstner T. M., Goodman

This database is a compilation of marine mammal and seabird information collected along the Pacific coast of the United States and U.S. territories in the Pacific from surveys that were solicited among regional research communities and persons. Information from standardized surveys was gathered from 2015 to 2018 and includes programs and researchers who collected information regarding seabirds since 1960.

This database is a compilation of marine mammal and seabird information collected along the Pacific coast of the United States and U.S. territories in the Pacific from surveys that were solicited among regional research communities and persons. Information from standardized surveys was gathered from 2015 to 2018 and includes programs and researchers who collected information regarding seabirds since 1960.

This datasets summarizes small mammal trapping efforts that USGS San Francisco Bay Estuary Field Station has led, co-led, or supervised, to detect and monitor the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in the northern reaches of San Francisco Bay from 1998-2014. As the salt marsh harvest mouse is listed as endangered under the Endangered Species Act, sensitive location information can be made available upon request by contacting the dataset point of contact.

Tracklines and associated observations were mapped and analyzed using ArcMap (ESRI, Redlands, CA). GPS data were recorded in NAD27 map datum and projected to an USGS Albers Equal Area Conic map projection for presentation and subsequent density analyses. Concatenated GPS and observation data were then used to generate point and line coverages in ArcMap (ESRI, Redlands, CA). We designed a custom analytic tool using ArcMap Model Builder that allows for the construction and export of user-specified and effort-adjusted spatial binning of species observations along continuous trackines. For the purposes of this report, we calculated seabird density estimates and marine mammal counts along continuous 3.0-kilometer and 7.7-kilometer trackline segments (i.e., 3.0 kilometer and 7.7 kilometer bins). Therefore, marine bird densities (at 3-kilometer scale, for example) are based on a composite strip area ranging from 0.15 per kilometer squared (one observer on effort) to 0.30 per kilometer squared (two observers on effort). We made no effort to adjust densities such that they would be proportional to variations in the area of buffered transect strip bin (i.e., weighted offset variable). These data are associated with the following publication: Mason, J.W., McChesney, G.J., McIver, W.R., Carter, H.R., Takekawa, J.Y., Golightly, R.T., Ackerman, J.T., Orthmeyer, D.L., Perry, W.M., Yee, J.L. and Pierson, M.O. 2007. At-sea distribution and abundance of seabirds off southern California: a 20-Year comparison. Cooper Ornithological Society, Studies in Avian Biology Vol. 33. References- ESRI. ArcGIS Desktop: Release 10. Redlands, CA: Environmental Systems Research Institute.

Broad survey lines, island radial survey lines, coastal survey lines, and focal-area (Santa Barbara Channel) survey lines were surveyed during each oceanographic season: spring (May), fall (September), and winter (January) during 1999 (May and September), 2000 (January, May, September), 2001 (January May, September), and 2002 (January). Aerial survey methods follow Mason et al. (2007). Specifically, we recorded all sightings of marine animals, vessels, and floating objects from twin-engine, high wing aircraft (Partenavia P-68s, Aspen Helicopters, Oxnard, CA, or California Department of Fish and Game) along pre-determined 100-meter (50 meters per side) strip transects at 60 meters above sea level. Surveys were flown at 160 kilometers per hour, and we used a Global Positioning System (GPS) unit linked to a laptop computer that allowed us to simultaneously collect coordinates (WGS-84 map datum), sea surface temperature (SST, degrees Celcius [°C]) determined via a belly-mounted, digital infrared radiation pyrometer (Heitronics™ KT19.85; measurement interval = 1 s, response time = 3 ms, emissivity = 0.99). SST values were appended to GPS flight data based on date and time. During individual surveys, observers frequently verified strip widths using hand-held clinometers. Observations generally were discontinued when glare exceeded greater than 25% of the field-of-view or if sea state exceeded Beaufort 5 (29–38 kilometers per hour wind speed). Observations were recorded into hand-held audio recorders. The third (non-dedicated) observer assisted the pilot with navigation, monitored sensor data, and maintained the onboard computer. The third observer also recorded incidental observations of marine mammals outside transects (i.e., non-standardized effort sightings). The effort for incidental marine mammal observations is not always consistent because the third observer was sometimes required to be engaged in other activities. Observations of species or individuals identified to nearest taxon included number of individuals, time, pre-coded behaviors, flight direction, and interspecies or vessel associations. Digital recordings of observations were archived and used by observers after surveys to enter data into a customized Graphical User Interface. Observation data were proofed after transcription to ensure accuracy or to resolve inconsistencies. Species observations were linked with GPS-based tracklines generated at 1 to 3 s intervals. Based on variations in the lag-time between sightings and recordings, we estimate that observations have a nominal along-trackline spatial accuracy of 222 meters, based on a five-second lag at 160 kilometers per hour survey speed. These data are associated with the following publication: Mason, J.W., McChesney, G.J., McIver, W.R., Carter, H.R., Takekawa, J.Y., Golightly, R.T., Ackerman, J.T., Orthmeyer, D.L., Perry, W.M., Yee, J.L. and Pierson, M.O. 2007. At-sea distribution and abundance of seabirds off southern California: a 20-Year comparison. Cooper Ornithological Society, Studies in Avian Biology Vol. 33.