About Our Monitoring Program
One of the primary goals of the Estuary Program is to understand conditions in the estuary and the lands that surround it. The Estuary Program has collected data for over twenty years that helps determine how different human and natural factors affect the health of Morro Bay. We share this data set with nonprofits, partner agencies, landowners, and the community to support our mutual goal to protect and preserve this unique area.
Our monitoring efforts strive to track long-term trends and to determine the effectiveness of specific conservation projects. High quality data is critically important for prioritizing future projects, evaluating the effectiveness of existing projects, and assessing long-term changes in health. Our work encompasses the entire Morro Bay watershed, which includes the estuary and the creeks that drain into it. Monitoring is conducted by staff and the community volunteers who make many of our monitoring efforts possible.
Updates from the Field
Every other month, our monitoring and research field staff share what they’ve been working on in a brief blog post. These posts highlight our ongoing projects, and give a glimpse into what our work in the field looks like. To learn more, be sure to check out the posts below, or visit www.MBNEP.org/blog.
Top Blogs of 2025: Happy New Year from the Estuary Program
Project Highlights
Each spring, staff and volunteers head out to local creeks to conduct bioassessment monitoring, a tool for evaluating creek health. During each survey we collect nearly 1,500 measurements that help us determine if the habitat can support sensitive aquatic species, including the steelhead which are native to our creeks.
One critical aspect of bioassessment monitoring involves collecting benthic macroinvertebrates (or “BMIs”), which are bottom-dwelling insects that are visible to the naked eye. The types of BMIs found in a creek tell you something about water quality. Some species are very sensitive to pollution, so their presence means the water quality is likely good. Others are very tolerant of pollution, which could indicate poor water quality.
The Estuary Program has conducted bioassessment in the Morro Bay watershed since 2002. This data helps us understand creek health and how conditions are changing over time. We use standardized protocols from the California Water Board’s Surface Water Ambient Monitoring Program (SWAMP). We ensure that data is widely available by posting it to the Water Board’s California Environmental Data Exchange Network (CEDEN).
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The Morro Bay watershed is home to a number of sensitive species, including Central Coast steelhead and the California red-legged frog. Freshwater creeks provide critical habitat for these sensitive species, as well as a diverse abundance of aquatic life. To sustain this complex ecosystem, the water in our creeks must be clean, cool, and well-oxygenated.
The Estuary Program has a dedicated group of community volunteers who collect creek water quality data each month. These volunteers collect readings of metrics like water temperature, dissolved oxygen concentration, water clarity, and stream flow. The resulting data help us track long-term trends throughout the watershed.
Estuary Program staff also deploy a network of continuous data loggers throughout the watershed. We program these devices to collect readings at regular intervals and then place them in the creeks. The resulting data allows us to better understand how water quality changes throughout a day and how conditions differ with the seasons. To read more about our continuous data loggers, you can visit this blog post.
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Morro Bay attracts visitors and locals alike, offering ample opportunities for recreation including sailing, swimming, fishing, birding, and paddling. In order for people to safely recreate, the waters must be free of pathogens like bacteria and viruses. Pathogens can come from sources such as stormwater runoff, pet waste, agricultural operations, marine wildlife, or sewage spills from treatment plants or waste-holding tanks on boats.
To assess safe swimming conditions in the bay, Estuary Program volunteers collect water samples from eight bay shoreline sites each month. The volunteers then analyze the samples at a laboratory to determine if the water is safe for recreational contact. This monitoring began in 2005, and thanks to countless hours from dedicated volunteers, has resulted in a long-running dataset that tracks the safety of swimming conditions in the bay.
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Data Availability
The Estuary Program collects year-round and seasonal monitoring data that help determine how different human and natural factors affect the health of Morro Bay. We rely on staff and trained volunteers to collect data. Our quality assurance information is documented our Quality Assurance Project Plan (QAPP). This document is reviewed and approved by EPA and the State Water Resources Control Board.
Data from our monitoring and research are summarized into technical memos and reports. To access these reports, please visit our library.
Most data is available for download from the California Environmental Data Exchange Network (CEDEN) at www.CEDEN.org, or from the California Open Data Portal at data.CA.gov. With any other data requests, please contact the Estuary Program.
Volunteer Opportunities
The Estuary Program occasionally recruits volunteers to support bioassessment and water quality monitoring efforts. For more information about volunteering with our program, please visit mbnep.org/volunteer.
