Spatial and Temporal Analysis of Fish Assemblages in Tidal Estuarine Habitats in the South Slough and Coos Estuary


Spring 2016 Project Update: The grant agreement for the project was completed in late August 2015.  During September-October, a reconnaissance assessment of sample sites was made, and two technicians were hired to sample in South Slough (monthly beach seining, fyke trap netting at Kunz Marsh, point water quality measurements).  An OSU/Forest Service team is conducting seasonal beach seining in upper Coos Estuary.  Two additional water quality monitoring stations were established in upper Coos Estuary to supplement system-wide stations in South Slough.  Two fyke trap nets will be set during November-February at Kunz Marsh.  Monthly sets of three nets (each in a cell representing high, mid, and low marsh elevations) were originally proposed at Kunz Marsh.  However, cells were found to represent two elevations so that two nets will be used, and the November-February period is consistent with previous sampling.  Kunz Marsh will be resampled in fall 2017.    Field work is ongoing and will span two full calendar years, beginning in January 2016.  The project has also afforded outreach opportunities engaging middle and high school students and teachers in the field.


Background: The Coos estuary is located in southern Oregon and is the second largest estuary in the state. Encompassing approximately 13,348 acres and capturing the drainage of 387,200 acres of upland, this large and complex estuary provides critical rearing habitat for dozens of marine and anadromous fishes and is home to many more resident fish species that spend their entire life cycle in estuarine habitats. Commercial fisheries have been critical to the economy of the region, and the Coos estuary has been an important system in recovery planning for endangered salmonids and estuarine restoration. 


Estuaries provide critical habitat for many marine, amphidromous, and resident estuarine fish species. While several studies document the importance of estuaries as rearing habitats for juveniles of individual species, much less work has focused on fish assemblages. The few studies that have examined estuarine fish assemblages are generally older, limited to short-term sampling periods, or utilize life-stage specific sampling gear. Because variability in habitat and water quality conditions can influence fish presence and abundance, long-term studies of fish assemblages are needed. For the Coos estuary in particular, a large data gap has already been identified for non-salmonid fishes in the estuary (Cornu et al. 2012; Partnership for Coastal Watersheds Coos Inventory Project).


Project Purpose: The primary purpose of this project is to characterize the temporal and spatial patterns of fish assemblages in the Coos estuary. This will be accomplished through three interrelated fish assessments. Broad-scale trends will be assessed using long-term fish sampling datasets throughout the Coos estuary. Fine-scale, monthly fish sampling in the South Slough will be combined with the collection of water quality data to examine trends in the fish assemblages related to environmental conditions over two sampling years. Seasonal sampling at locations in the upper region of the Coos estuary will allow for spatial comparisons between fish communities in two distinct regions of the estuary.


The goal of this project is to better understand the current and past distribution patterns of fish that use habitats in the Coos estuary. This project will answer critical questions about fish assemblage distribution and diversity and species-specific habitat use and requirements of resident and migratory fish in the Coos estuary. A better understanding of how different fish species use the estuary, and of changes in those fish species over time, is critical for the informed management of the Coos estuary. This information is needed to better inform permitting for current and future shoreline development proposals and will contribute to estuarine habitat conservation, restoration, and compensatory
mitigation planning. We will synthesize information into formats that are easily accessible to scientists, land managers, decision makers, planners and community stakeholders to facilitate the integration of our findings into strategic and ecologically driven conservation planning for commercially and recreationally important species, as well as culturally and ecologically valuable species.


Project species: Dungeness crab, English sole, starry flounder, shiner perch, steelhead, coho salmon, Chinook salmon, brown rockfish, staghorn sculpin. In addition, 75 fish species have been documented in the Coos estuary and include: American shad, Arrow Goby, Bay Goby, Bay pipefish, Black Rockfish, Blennies, Blue Rockfish, Bocaccio, Brown Irish Lord, Brown Rockfish, Buffalo sculpin, Cabezon, Chinook salmon, Chum salmon, C-O Turbot, Coho salmon, Copper Rockfish, Crescent Gunnel, Curlfin Turbot, Cutthroat trout, English Sole, Green Sturgeon, High Cockscomb, Jacksmelt, Kelp Greenling, Large scale sucker, Lingcod, Longfin Smelt, Longnose dace, Mosshead sculpin, Northern anchovy, Pacific herring, Pacific lamprey, Pacific Sablefish, Pacific Sand Lance, Pacific Sanddab, Pacific Tomcod, Padded Sculpin, Penpoint Gunnel (green), Pile Perch, Pink Salmon, Plainfin midshipman, Prickly sculpin, Rainbow Perch, O. Mykiss (Rainbow trout and Steelhead), Red Irish Lord, Red Tailed Surf Perch, Redtail Perch, Rex Sole, Rock Greenling, Rock Sole, Rockweed Gunnel, Saddleback Gunnel, Sand Sole, Sardine Pacific, Sharpnose sculpin, Shiner perch, Silver (surf) Perch, Silver spotted Sculpin, Snake Prickleback, Speckled dace, Speckled Sanddab, Staghorn sculpin, Starry flounder, Striped bass, Striped Seaperch, Surf smelt, Threespine stickleback, Tidepool Sculpin, Tidepool Snailfish, Topsmelt, Tubenose poacher, Tubesnout, Walleye Perch, White Seaperch, Whitebait smelt


Metrics to evaluate success: 

  • The establishment of an in-house database for fish data collected in South Slough and upper Coos estuary from 2015-2017
  • Water quality data collected at all sites will pass the quality assurance/quality control metrics established by the Centralized Data Management Office of the National Estuarine Research Reserve System (NERRS)
  • Data from the established long-term water quality monitoring stations in South Slough will be uploaded to the publically-accessible NERRS website; because the upper Coos estuary water quality stations are not long-term stations (required by the NERRS), data from these sites will be housed in an in-house database and made available upon request.
  • Data summaries will be uploaded to the Partnership for Coastal Watersheds website, which is currently in development and will house data summaries and analyses for the Coos Estuary Inventory Project.
  • Project results will be summarized and incorporated in training workshops for coastal decision makers and managers, coordinated by the Coastal Training Program at the South Slough National Estuarine Research Reserve.
  • Data from the project will be used to create a data analysis learning module for high school students, designed to meet grade-level curriculum requirements and complement hands-on learning opportunities for high school students volunteering in the field work of this project.
  • Results from the project will be reported in a manuscript and submitted for publication to a peer-reviewed journal.
  • Results will be presented at professional meetings and academic seminar series.

Climate change strategies addressed by this project:

3.2 Promote habitat connectivity and integrity.

3.3 Reduce non-climate change ecosystem stressors.

3.5 Conserve coastal and marine resources.


National Conservation Strategies addressed by this project:

  1. Protect intact and healthy waters.
  2. Reconnect fragmented fish habitats.
  3. Restore water quality.


 Project area map  Upper Coos Estuary Project

South Slough Estuary Project

Top left photo: Project area map, showing the Coos estuary and delineation of zoomed views for South Slough (A) and upper Coos estuary (B). Top right photo: Upper Coos Estuary Project Area. Orange triangle is upper Coos estuary sites. Yellow circles are historical sites. Bottom left photo: South Slough Project Area. Orange triangles are 1987 seine sites; brown triangles are additional seine sites; green polygon is Kunz Marsh fyke sites; yellow circles are historical sites; and the white polygon is the South Slough Reserve Boundary.

Valino View

Logan Marsh

fish i n South Slough

field work in south slough


south slough sampling     southsloughsampling2

southsloughsampling3     southsloughsampling4

The four photos above show teachers participating in Fishing the Tides, a training program designed to provide teachers and middle and high school students with meaningful experiences collecting and investigating historic and current fish data in the Coos estuary. They will work with scientists to analyze ecological changes in the estuary. Training program data is contributing to the spatial and temporal analysis of fish assemblages in the Coos estuary.