San Francisco Bay Dredging Projects – Is That Eelgrass in your Footprint?

by Gwen Santos

Spring has arrived and that means the season for dredging and other in-water work in San Francisco Bay is just around the corner.  Do you know what’s in your subtidal footprint?  If eelgrass (Zostera marina or Z. pacifica) or other submerged aquatic vegetation (SAV) is present, pre- and post-project surveys are typically a requirement of environmental permits.

Keeping apprised of your environmental permitting requirements will keep your project on schedule and within budget.  Below are ways to navigate your project’s permitting process to assure compliance with the regulatory agencies:

  1. Understand regulatory agency requirements for pre-project surveys.  Typically, these surveys are required to be conducted prior to project work to determine the location and density of eelgrass or other SAV.
  2. Schedule surveys.  While peak growing season is July and August, surveys can be scheduled between May and September in the San Francisco Bay and between April and October in other parts of California.  Choosing the appropriate survey technique is important for receiving agency approval, accurate mapping, and balancing cost.
  3. Plan for mitigation.  If eelgrass or SAV is present in or near your project footprint, you may be required to implement minimization measures to reduce potential impacts.  Minimization measures include actions to limit turbidity, light reduction, sediment loading, and circulation patterns by minimizing scouring velocities near eelgrass or SAV beds.  If your project impacts eelgrass, mitigation is typically required in the form of transplantation or seeding.

Eelgrass Significance in the Bay


Eelgrass (Zostera marina or Z. pacifica)


Eelgrass is an important foundation species in San Francisco Bay that provides habitat for commercially important significant and endangered fish, and as well as invertebrates such as crabs, shrimp, and sea slugs, which provide food for other marine species.  Eelgrass and other SAV also provides less observable environmental services including water filtration and sediment stabilization which help improve the overall health of the San Francisco Bay.

Human activities have historically impacted eelgrass habitats including nearshore development, surface scouring, and dredging, therefore these habitats have been identified as habitat areas of particular concern by the Pacific Fishery Management Council.  The National Oceanic and Atmospheric Administration (NOAA) and the National Marine Fisheries Service (NMFS) developed the California Eelgrass Mitigation Policy and Implementing Guidelines in 2014 which provides guidelines for surveying, minimizing impacts, and mitigation recommendations for unavoidable impacts.

Regulatory agencies require pre- and post-project surveys to mitigate potential impacts to eelgrass and other SAV because of the essential ecosystem services eelgrass and SAV provide.

Surveying Techniques to Mitigate Potential Impacts

Dredging and other in-water work has the potential to impact eelgrass and SAV.  Pre-disturbance surveys can identify eelgrass and SAV located in the project footprint that might be impacted.

The ideal survey period for eelgrass and SAV is during July and August, which marks the peak growing season (generally May through September for Northern California). Post-project surveys are used to quantify impacts (if any) and are typically required by the regulatory agencies to determine mitigation.

NOAA and NMFS recommend varying survey techniques, including visual or acoustic methods appropriate to the action, scale, and area of work. WRA recommends using side-scan sonar (acoustic method) for large, multi-acre projects, and foot/kayak surveys (visual method) for smaller and subtidal projects.

Side-Scan Sonar

Side-scan sonar is a technique frequently employed to cover large areas of potential habitat (think Caltrans San Francisco-Oakland Bay Bridge Project) and therefore may the most cost-effective and efficient method to determine pre- and post-disturbance impacts from dredging.  In some cases, the use of side-scan sonar is required by the natural resource agencies.

GIS figure showing eelgrass or SAV density in a project footprint.

GIS figure showing eelgrass or SAV density in a project footprint.

Side-scan sonar uses transmitted sound energy to create a picture of the subsurface.  A towfish housing the sonar scanning equipment is mounted to a small boat.  The vessel then proceeds along the project footprint, scanning the subsurface.  Varying intensity of percent coverage of eelgrass is depicted in the final product.  The data can then be imported in to GIS software to produce a figure showing eelgrass or SAV density in the project footprint.

For smaller project areas, the subtidal surveys can be completed on foot, visually identifying eelgrass using a GPS unit.  The end-product is similar to that of the side-scan sonar, with density, number of individual plants, and patch/bed area reported.


Contact us to schedule your survey and keep your project on track and in compliance with the regulatory agencies. This article is also featured in the Bay Planning Coalition’s April 2015 Newsletter.