Preserving Secret Harbor Salt Marsh and Estuary

The Cypress Island Natural Resource Conservation Area (NRCA) and Aquatic Reserve remains one of the first conservation areas established following the 1987 Natural Resources Conservation Areas Act created by the Washington State Department of Natural Resources (DNR). A part of the San Juan Islands in Western Washington, this conservation area spans over 6000 acres, protecting forests, wetlands, grasslands, and surrounding tidelands. DNR is the current steward of the state-owned uplands and aquatic lands of the Cypress Island  NRCA, Aquatic Reserve, and the Cypress Highlands, Natural Area Preserve (NAP). As steward, DNR manages the NRCA and NAP recovering and preserving natural ecological systems, while providing recreational opportunities to the public.

In alignment with these conservation efforts, Herrera worked with DNR on restoration, access planning, and education design of the Secret Harbor salt marsh and estuary on the northwest side of Cypress Island. Herrera conducted a feasibility study, designed restoration features and corrective actions, prepared a monitoring plan, and provided permitting assistance. Project objectives included restoring hydrologic connection and nearshore processes to the estuary and adjacent freshwater wetlands and streams, in addition to providing a continuum of upland, riparian, freshwater, and saltwater habitats within the 28-acre site and therefore also improving the larger Secret Harbor basin which is more than a square mile in area. Through this work, Herrera is helping to preserve natural environmental conditions, while providing additional low impact public use opportunities and environmental education.

Existing Conditions

The Secret Harbor project site included a freshwater wetland complex and a salt marsh that was separated by a 300-foot dike. The dike contained a culvert which allowed marine inundation, at some tidal ranges, to enter the remaining salt marsh from an estuarine pond. The pond was bordered by Secret Harbor Road, which physically separated the freshwater wetland complex from the salt marsh and estuarine pond. A culvert located beneath the road carried freshwater from upstream and from the freshwater marsh into the estuarine pond.

Freshwater sources included hillside seepages, natural drainage from complex wetland areas, and a historic perennial stream, which had been altered by past ditching. The existing infrastructure limited wetland structure and function and unnaturally modified instream flow rates and freshwater discharge to Secret Harbor. Additionally, runoff was stored in existing stock ponds, sewage lagoons, and a landfill. Previous restoration site efforts to remediate soils had left other disturbed upland areas, where building and facilities were previously removed.

Feasibility Study

To assess the historical and existing physical and ecologic conditions at the site, Herrera’s team conducted a collaborative year-long study to characterize factors that influence the site and its associated habitat features. Processes and conditions evaluated in this study include coastal and estuarine geomorphology, human modifications, topographic survey, hydrologic conditions and upland watershed assessment, hydrogeomorphic  assessment of ecological function, analysis of reference sites, fish habitat and use, and cultural resources assessment.


From these observations, Herrera described the alteration of estuarine and wetland areas. These effects on the site’s geomorphic characteristics were caused by channel simplification and the placement of dikes, fill and undersized culverts that restricted estuarine circulation. Due to restricted circulation, transport of sediment and marine organic detritus were disrupted, in addition to causing stratification of the estuarine pond leading to poor water quality and algal blooms. Flow control structures were also in disrepair, with failed structures causing further ecological damage and disturbance. These results were used in the team’s alternative analysis to develop a comprehensive solution focused on improving and restoring estuarine conditions throughout Secret Harbor.

Designing a Solution

Herrera’s team provided DNR with three alternative solutions to choose from. The chosen design included:

  • Restoring natural beach conditions through fill removal and excavating a distributary channel network within the historic salt marsh.
  • Removing an existing dike.
  • Dredging and regrading the creek channel bed and geometry located within the estuary.
  • Breaching the dike and rehabilitating creek flow to the Secret Harbor estuary.
  • Filling a freshwater drainage ditch to improve wetland hydrology.
  • Removing a road prism and culvert within the fresh water wetland.
  • Removing a failed concrete bulkhead and concrete debris from beach.

Education and Access

In addition to the ecological function improvements, experimental public education and access opportunities were proposed to further enhance the site, as an amendment to the original work. These components consisted of transforming historic roads into a more formal trail system and installing a composting toilet to introduce site users to green technology. After discussions with the DNR and its stakeholders, including the Samish Indian Nation, a low-impact strategy was adopted for developing the trail network. Trail system components included an 8-foot-wide main path for authorized vehicles, eliminating several informal, existing trails to direct pedestrian traffic away from restored areas, and converting informal, 3-foot-wide trails specifically for pedestrian use where they connected to important features on the island. To improve drainage, water bars and culverts were added to the main trail. Trails were named to tell the story of previous land use, providing a focused curriculum on the culture and history of Cypress Island, particularly its relevancy for the Samish Indian Nation and their ancestors. By utilizing historic roads, trail users are connected to relevant locations, while minimizing the impacts for trail infrastructure.

Paving the Way

During the commencement of this project Herrera provided permitting support, including permit level drawings which met the requirements of the various permitting agencies that use the Joint Aquatic Resources Permit Application (JARPA) form. During construction, Herrera’s team provided constructability review, bid support, and construction oversight. By value-engineering the project design, Herrera helped DNR minimize construction costs through the recycle and reuse of suitable fill materials.

Monitoring Plan

To ensure ongoing success, Herrera developed a comprehensive monitoring plan to inform and evaluate future corrective actions that may be required to meet performance standards and plan objectives. Monitoring actions include site visits by the Samish Indian Nation, in coordination with DNR, to understand the need for corrective action, such as native plant mortality, establishment of noxious plant species, erosion, problems with the water regime, or other factors. These efforts will ensure the long-term vitality of Secret Harbor, meeting the projects goal to recover and preserve natural environmental conditions, while providing recreational and educational opportunities for the public.