Elkhorn Slough National Estuarine Research Reserve: Fish surveys
Data files
May 08, 2026 version files 3.20 MB
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Data_Dictionary.csv
1.87 KB
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Elkhorn_Slough_Map.kmz
1.03 MB
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Fish_Metadata.pdf
154.88 KB
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Fish_Survey.csv
1.89 MB
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Notes.csv
3.29 KB
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README.md
11.54 KB
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Supplemental_Info.csv
100.24 KB
Abstract
This dataset documents long-term fish monitoring in Elkhorn Slough from 1964 to present, capturing species diversity, abundance, and size across 29 sites. It integrates contributions from multiple institutions, including but not limited to Moss Landing Marine Laboratories and the Elkhorn Slough National Estuarine Research Reserve, with historical data (1964–2003) compiled by Monterey Bay National Marine Sanctuary. The dataset includes species identifications, counts, and occasional length measurements. Fish were captured using varying methods, identified, measured, and released. This dataset supports analyses of long-term ecological change and restoration effects, though users should account for variation in sampling methods and effort over time.
Dataset DOI: 10.5061/dryad.k6djh9wnh
Description of the data and file structure
Fish surveys in Elkhorn Slough are conducted to document long-term patterns in species diversity, abundance, and sizes across the estuary. Sampling has occurred since 1964 through a combination of research projects, academic field courses, and monitoring programs led by multiple institutions, including Moss Landing Marine Laboratories and Monterey Bay National Marine Sanctuary. Surveys were designed to characterize fish communities across a range of sites and time periods. Fish are captured using a variety of gear types, then identified to species, counted, and in some cases measured before being released.
Files and variables
File: Data_Dictionary.csv
Description: An explanation of several columns. All other columns (ie date, species, etc.) are intuitive and thus not explained in the data dictionary table.
Variables
- Column name: A list of some of the names of columns in the dataset that may not be intuitive.
- Description: A description of what is in aforementioned columns.
File: Fish_survey.csv
Description:
This dataset contains fish survey records collected between 1964 and 2025. Because the dataset is a compilation of surveys conducted by many researchers and organizations over several decades, sampling protocols, datasheets, recorded variables, and levels of detail were not fully standardized across all sampling events. As a result, not every variable is populated for every record.
NA (“Not Available”):
Values marked as “NA” indicate missing data for a given variable and sampling event.
Null Values in Location Fields (Columns G–I):
Null values are used exclusively within the location hierarchy columns (G, H, and I). Location information was standardized and curated to align with the large-scale site map provided in the accompanying KMZ file. Because not all geographic regions contain corresponding subregions, areas, or subareas, some hierarchical location fields are intentionally left null. In these cases, “null” does not indicate missing data; rather, it signifies that no applicable site designation exists for that level of the hierarchy.
Variables
- Date: The date that the sampling event took place (YYYY-MM-DD).
- Year: The year that the sampling event took place (YYYY).
- Month: The month that the sampling event took place, as designated by a number (ie January = 1, February = 2, etc.).
- Season: The season that the sampling event took place (autumn, spring, summer, winter).
- Region: Large-scale location category in Elkhorn Slough, see KMZ file provided separately.
- Subregion: finer categorization of region used by ESNERR; see KMZ file provided separately.
- Area: Locations within "Regions" of Elkhorn Slough, see KMZ file provided separately.
- Subarea: finer categorization of area used by ESNERR; see KMZ file provided separately.
- Site_Notes: Any notes associated with the location of the survey.
- Time_Original: The time as stated in the historic dataset. Time is listed either as a range (beginning to end of sampling) or as a singular time. Time format varies widely and can include HH, HHMM, HH:MM, HHMM-HHMM, HH:MM-HH:MM, HH-HHMM, HHMM-HH, HH-HH:MM, HH:MM-HH, etc.
- Start_Time: Start time of survey. New column made during data curation for standardization (HH:MM).
- End_Time: End time of survey. New column made during data curation for standardization (HH:MM).
- Collected_By: Which organization conducted the survey (ie MLML, ESNERR, etc.).
- Species: Species of fish identified.
- #_Individuals: Number of individuals surveyed for that particular species.
- Method1: The primary type of equipment used during the survey.
- #_Method1: Indicates how many times the equipment was used during that survey, or the number of individual units deployed. For example: if Method #1 is a beach seine and # of Method #1 = 3, the seine net was pulled three times that day; if Method #1 is a box trap, three box traps were deployed.
- Method2: If a second type of survey equipment was used on the same day, it is listed here.
- #_Method2: Indicates how many times the equipment was used during that survey, or the number of individual units deployed. For example: if Method #2 is a beach seine and # of Method #2 = 3, the seine net was pulled three times that day; if Method #2 is a box trap, three box traps were deployed.
- Creel_Y/N: “Y” indicates a creel survey, where researchers collected data directly from anglers at boat ramps or shorelines. “N” indicates the data are not from a creel survey.
- Method_Notes: Any additional notes associated with the survey method and/or equipment.
- General_Notes: Any other notes, which may include information on tagging, uncertainty in species ID, pregnancy, or other observations.
- #_Fishermen: Number of fisherman sampled, if this survey is a Creel survey.
- Time_Sampled(mins): How long surveyors spent sampling (minutes).
- Distance_Sampled(nm): How far offshore surveyors spent sampling (nm).
- Speed_Sampled(knots): How fast the sampling vessel moved through the water (knots).
- Depth_Min(ft): Minimum depth of water during sampling (ft).
- Depth_Max(ft): Maximum depth of water during sampling (ft).
- Bait: Bait used to attract fish for that survey.
- Size(Historic): All fish sizes from the historic dataset (1964-2003). These were too complex to fully integrate into the current dataset (which has 10 size columns per species in cm), so historic sizes remain as-is, in their own column. Units are generally listed either in this column or in "size notes" and can include in, ft, mm, cm, or visual descriptors.
- Size1(cm): Include sampling dates from 2010 and on. This is the size of the first individual fish that was measured (cm).
- Size2(cm): Include sampling dates from 2010 and on. This is the size of the second individual fish that was measured (cm).
- Size3(cm): Include sampling dates from 2010 and on. This is the size of the third individual fish that was measured (cm).
- Size4(cm): Include sampling dates from 2010 and on. This is the size of the fourth individual fish that was measured (cm).
- Size5(cm): Include sampling dates from 2010 and on. This is the size of the fifth individual fish that was measured (cm).
- Size6(cm): Include sampling dates from 2010 and on. This is the size of the sixth individual fish that was measured (cm).
- Size7(cm): Include sampling dates from 2010 and on. This is the size of the seventh individual fish that was measured (cm).
- Size8(cm): Include sampling dates from 2010 and on. This is the size of the eighth individual fish that was measured (cm).
- Size9(cm): Include sampling dates from 2010 and on. This is the size of the ninth individual fish that was measured (cm).
- Size10(cm): Include sampling dates from 2010 and on. This is the size of the tenth individual fish that was measured (cm).
- Size_Notes: Any additional notes associated with the sizes of the organisms.
- FLAG: Indicates flagged rows. See Notes.CSV or Metadata document for details on flag codes.
File: Notes.csv
Description: Read these notes for key information before working with the data.
Variables
- A list of notes including general notes, historical data notes, taxonomic notes, additional resources, and flag codes.
File: Supplemental_Info.csv
Description: Additional data (environmental conditions, notes, etc.) for some of the historic data. Note that not all surveys are represented here.
Variables
- Date: Date of survey, either written as M/DD/YYYY or MM/DD/YYYY.
- Distance_Offshore: Distance from the survey vessel to the shoreline. Units are within the cell and can include yards, mile, feet, or general descriptions of the channel.
- Bottom_Depth(ft): Depth to the bottom of aquatic sampling location (ft).
- Bottom_Type: Description of the physical characteristics of the bottom substrate.
- Water_Temp: Temperature of the water. Units
- Water_Clarity: Description of how clear the water was on that sampling day.
- Salinity(ppt): Salinity measurement of the water, in ppt.
- Tide: Description of nature of tide (high, low, etc.).
- Current: Description of how strong the current was.
- Sea_Condition: Notes of the sea condition (calm, no waves, etc.)
- Air_Temp: Temperature of the air.
- Weather: Notes on the weather during sampling.
- Vegetation: Notes of any particular species of vegetation identified during sampling.
- Record#: Number given to each individual record at the time of entry into the database. An individual record is a single datasheet and all the information contained on it. Sometimes there is more than one sampling event per record. The record number simply pertains to the physical record of the data and is to facilitate going back to the hard copies to double check data in the future.
- Notes: Any other notes cited during sampling.
File: Fish_Metadata.pdf
Description: This file provides detailed metadata for Elkhorn Slough fish surveys, including research objectives, sampling methods, site information, data structure, and variable definitions. It also documents data sources, contributing institutions such as Moss Landing Marine Laboratories and Monterey Bay National Marine Sanctuary, as well as data quality procedures and guidance for appropriate use and interpretation.
File: Elkhorn_Slough_Map.kmz
Description: This is a google earth file showing how the Elkhorn Slough National Estuarine Research Reserve subdivides the estuary in to regions and areas that are included as columns in the dataset
Code/software
There is no special software needed for the CSVs, but you will need Google Earth to view the KMZ of the Elkhorn Slough map.
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- Elkhorn Slough National Estuarine Research Reserve (integrated historic data with our internal data, spanning 2010 to now).
- Monterey Bay National Marine Sanctuary (curated data from surveys 1964-2003).
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Barry, J., 1983. Utilization of shallow marsh habitats by fishes in Elkhorn Slough, California. MS Thesis, San Jose State University. 95 pp.
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Bennett, T., 1993. Resource partitioning of two fish ectoparasites, Lironeca vulgaris and Lironeca california (Class Isopoda, Family Cymothoidae). MS Thesis, San Jose State University. 46 pp.
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Brown, J., 2003. An evaluation of the nursery role of estuaries for flatfish populations in central California.. PhD Thesis, University of California Santa Cruz.
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Creel Census (funded by Pacific Gas and Electric), 1974-1976.
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Hall, M.A., 2000. Species composition and temporal and spatial characteristics of fish assemblages surveyed at Old Salinas River and Bennett Slough, California. Senior Thesis, Southampton College, Long Island University. 54 pp.
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Lindquist, D., 1998. The effects of erosion on the trophic ecology of fishes in Elkhorn Slough, California. MS Thesis, California State University Hayward. 65 pp.
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Moss Landing Marine Laboratories records of class field trips, class projects, and visiting groups (1964-present)
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Oxman, D., 1995. Seasonal abundance, movements, and food habits of harbor seals (Phoca vitulina richardsi) in Elkhorn Slough, California. MS Thesis, California State University Stanislaus. 125 pp.
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Sampling methods have varied considerably over time, largely depending on which of the entities conducted the survey. Below is a comprehensive summary of documented capture methods, along with general descriptions of the associated methodology.
- Seine (Seine, Beach seine, Minnow seine, Common sense seine)
- This method involves deploying a net to encircle fish in shallow water. The net is typically weighted along the bottom and supported by floats along the top. It is pulled by hand- either by wading surveyors or from shore- to surround and concentrate fish into a central “purse” or cod end for collection. Variations differ primarily in size, mesh, and deployment location (shore-based vs. in-channel), but all function as active encircling nets.
- Gill Net
- A passive entanglement net in which fish swim into the mesh and become caught, usually by the gills. Nets may be set vertically in the water column, either anchored to the substrate or suspended with buoys. They are typically left in place for a standardized period before retrieval. Mesh size and time interval may have varied historically.
- Trawl (Otter trawl, Channel net)
- A boat-deployed net that is either towed through the water column or set within a channel to intercept fish movement. Otter trawls use paired boards to hold the net mouth open while being pulled. “Channel net” references likely describe a similar large net deployed from a vessel. Specific configurations and target depths may have varied among surveys.
- Hook and Line (Hook and line, Long line, Line, Jigs, Gaff)
- Capture using baited hooks or artificial lures attached to a fishing line. This may include rod-and-reel angling, hand lines, or longlines with multiple hooks set along a main line. Gear may be actively fished (e.g., jigging) or passively set for a period before retrieval. A gaff may have been used as a landing tool for larger fish.
- Passive Traps (Minnow trap, Round trap, Collapsible box trap, Crab trap)
- Enclosed traps designed to allow fish to enter through funnel-shaped openings but limit their ability to exit. These traps are typically baited and deployed for a fixed time before retrieval. Designs and materials likely varied, and some traps (e.g., crab traps) may have captured fish incidentally.
- BRUV
- Baited Remote Underwater Video systems involve deploying an underwater camera system with bait to attract fish into view. The unit records for a standardized duration, after which footage is reviewed to identify species and estimate relative abundance. This method does not physically capture fish.
- Diver / Manual Capture (Spear, By hand)
- Active, selective capture methods conducted by individuals in the water. Fish may be taken using a handheld spear or speargun, or captured manually without gear. These methods are typically opportunistic and may be associated with shallow water or diver-based surveys.
- Fisher-Reported (Fisherman, Creel survey)
- Data derived from recreational or other anglers rather than standardized scientific sampling gear. This may include direct recording of fish caught by fishermen or interviews conducted as part of creel
- Other / Unspecified (Baited burlap bag, Shovel)
- Methods that do not clearly fit standard gear categories. A baited burlap bag likely functioned as an attractant device to draw fish into a confined area for capture. “Shovel” likely refers to manual substrate disturbance or excavation that resulted in incidental fish capture. Specific techniques were not consistently documented.
Regardless of the capture method used, all surveys require careful handling of collected fish to minimize stress and injury. Once nets or gear are retrieved- either to shore or aboard a vessel- fish are promptly transferred into large containers filled with seawater. Individuals are then identified to species and counted. Fish are handled either by hand or with a small dip (butterfly) net, depending on size and sensitivity. A subset of individuals is measured to obtain length data, and all observations are recorded on standardized data sheets before the fish are released back into the water. This summary does not include the various crab traps that were occasionally deployed specifically to survey crab populations alongside fish sampling efforts.