San Diego Regional Harbor Monitoring Program
How do we sample and assess the quality of harbor habitats in the San Diego region?
What is RHMP?
The San Diego Regional Harbor Monitoring Program (RHMP) is a collaborative network of stakeholders and scientists whose goal is to understand the quality of water, sediments, and aquatic life across four embayments in the San Diego region. Surveys occur on a 5-year cycle.
Photo: Sediment grab in North San Diego Bay
What locations are sampled?
Water, sediment, and the seafloor biological community are sampled in four Southern California embayments in the San Diego region: Dana Point Harbor, Oceanside Harbor, Mission Bay, and San Diego Bay.
Photo: Survey crew in Mission Bay recovering a sediment grab
A total of 75 stations are assessed for water and sediment quality, while 15 stations are assessed for the seafloor community including fish, crabs, lobsters, shrimp, sea stars, sponges, and more.
Photo: Surface conditions in Dana Point Harbor
Sediment stations are classified into five different strata to help determine what kind of natural and human activities may influence the quality of the habitat in each area: deep, freshwater-influenced, marina, industrial/port, and shallow.
Photo: Trawling for bottom dwelling organisms at sunrise in Oceanside Harbor
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Dana Point Harbor
Shallow recreational harbor with marinas, shops, restaurants, a marine science center, and a small public sandy beach (Baby Beach). Dana Point Harbor, built in the late 1960’s, has approximately 2,500 commercial and recreational boat slips in an area encompassing approximately 220 acres. With the exception of Baby Beach, the entire perimeter of the harbor is surrounded by a rocky boundary referred to as riprap.
4 sediment/water stations
1 seafloor community station
2
Oceanside Harbor
Shallow harbor area with shops, restaurants, and marinas. Shared semi-enclosed harbor with Marine Corps Base (MCB) Camp Pendleton. Oceanside Harbor, built in 1963, has approximately 800 commercial and recreational boat slips in an area encompassing approximately 70 acres (excluding the MCB). The entire perimeter of Oceanside Harbor is surrounded by a riprap boundary.
4 sediment/water stations
1 seafloor community station
3
Mission Bay
Mission Bay is a natural shallow embayment that has been modified by dredging and filling operations that occurred in the late 1940s. Mission Bay is a popular recreational area, with six marinas, several resorts, a golf course, and the Sea World Marine Park, all within its immediate boundaries covering an area of approximately 3.9 square miles. A mixture of sandy beaches and riprap line its 27 miles of shoreline. Three creeks provide freshwater influence within the eastern portion of Mission Bay. Much of the bay bottom is covered in eelgrass beds.
9 sediment/water stations
3 seafloor community stations
4
San Diego Bay
San Diego Bay is the largest estuary in Southern California encompassing an area of approximately 17 square miles (15 miles in length and 0.2 to 3.6 miles in width). It is a natural embayment that has been modified significantly over time by dredging and filling operations beginning in the early 1900s. It is the only harbor in the RHMP with industrial/port activity including a large working waterfront, several military facilities, and the adjacent San Diego International Airport. Numerous commercial and recreational marinas, as well as several offshore anchorages are located within the bay. There are approximately 200 municipal storm drains as well as six urban rivers/creeks that contribute watershed inputs into San Diego Bay. The larger size and multiple uses of San Diego Bay create unique environments that vary greatly from the mouth to the southern portion of the bay as highlighted below.
5
North San Diego Bay
Deep transition zone from open coastal to protected bay habitats with large marinas and a downtown waterfront. Some eelgrass beds and kelp located along the predominantly rocky (riprap) shoreline interspersed with a few sandy beaches along Point Loma and Shelter Island. Many pier pilings are located within the marinas and downtown areas.
20 sediment/water stations
4 seafloor community stations
6
Central San Diego Bay
A variable habitat with deep areas in a central channel and along the east side of the bay with heavy industrial activity, and shallower areas with eelgrass beds predominantly on the west side of the bay. The shoreline consists of mixture of riprap, pier pilings, and cement or steel barriers (quay walls) on the east side of the bay, and a mixture of riprap, pilings, and sandy beaches on the west side of the bay Three creeks (Switzer, Chollas and Paleta Creek) provide intermittent freshwater flows entering the east side of the bay among the shipyards.
22 sediment/water stations
2 seafloor community stations
7
South San Diego Bay
Shallow with extensive eelgrass beds and wetland areas. Two marinas on either side of the bay and freshwater influence from both the Sweetwater River and Otay River.
16 sediment/water stations
4 seafloor community stations
What are the physical conditions of the water?
Various sensors are used to measure water quality indicators like temperature, pH, salinity, clarity, and dissolved oxygen both at the surface and throughout the water column. Handheld meters are used for surface conditions, and a Conductivity-Temperature-Depth (CTD) instrument is deployed to look at these parameters through the entire water column.
Photo: Reading data from sensors deployed near the surface with a CTD on deck
How clean is the water?
Samplers, like this Niskin bottle, are used to collect water samples at any desired depth within the water column. Samples for the RHMP are collected 1 meter below the surface and are analyzed for nutrients, metals, oil, and other petroleum-based compounds.
Photo: Collecting water from a Niskin bottle for chemistry analysis
Filtering water to remove small particulates for analysis of dissolved metals
How do we study the seafloor?
While not visible from the surface, the health of the seafloor and associated animals is an important aspect of ensuring quality habitat in regional bays and harbors. In order to study the sediments on the seafloor, we first need to bring them up to the surface using grab samplers like the Van Veen grab shown here.
Video: Deployment and recovery of a Van Veen sediment grab sampler in Mission Bay
Begin Processing the Sediment Sample
Once the sediment grab is on deck, photos and notes about the appearance are taken before the sediment is disturbed. Examples of things noted are the presence of animals or vegetation, the consistency, odor, and color of the sediment, as well as any evidence of trash or debris.
Photo: Sediment grab on deck with station notes
Collect Sub-Samples
Surface sediment is then collected from the Van Veen grab. These samples are analyzed for physical characteristics (grain size, organic carbon content), toxicity, and chemical characteristics (i.e., metals, oil and other petroleum-based compounds, pesticides, polychlorinated biphenyls [PCBs], and other chemicals of emerging concern such as fire retardants).
Photo: Sampling the sediment surface for chemical and physical characteristics
What lives on the seafloor?
Animals that burrow into the sediment are called benthic infauna. Animals that live on top of the sediment are called benthic epifauna.
Video: Look closely – the sediments are alive!
Benthic infauna observed in the sediment grab samples are collected, identified, and counted.
Photo: Sediment grab in Mission Bay with sand dollars and sea pens visible on the surface
The benthic infauna collected are diverse and numerous, with 414 species collected in 2018.
Photo: Sand dollars, sea pens, mussels, and razor clams
Sediment is washed through a sieve on deck
All organisms remaining on the sieve are collected and identified down to the lowest practical taxon
What fish and other animals live on the seafloor?
Fish and large invertebrates (such as lobsters, crabs, shrimp, sea stars, etc.) live on the seafloor and are identified using a large trawl net that travels across the surface of the seafloor.
Photo: Crew retrieving an otter trawl net in Mission Bay capturing species living on the seafloor
Animals collected in the net are brought on deck and sorted into bins with fresh seawater. They are then measured and weighed before being released.
Photo: Placing catch into bins with seawater for sorting
Spotted Sand Bass (Paralabrax nebulifer)
California Halibut (Paralichthys californicus)
Trawls catch a high diversity of large invertebrates, with 47 species identified in 2018.
Video: A heart urchin (Lovenia cordiformis)
California Spiny Lobster (Panulirus interruptus)
Target Shrimp (Sicyonia penicillata)
Gorgonian, a type of soft coral (Muricea sp)
Bat stars (Patiria miniata)
Trawls also capture a diverse assemblage of fishes, with 32 species captured in 2018.
Photo: Pacific Seahorse (Hippocampus ingens)
Gopher Rockfish (Sebastes carnatus)
Horn Shark (Heterodontus francisci)
California Tonguefish (Symphurus atricaudus)
Black Croaker (Cheilotrema saturnum)
Northern Anchovy (Engraulis mordax)
Test samples in the lab
Sediments are taken to the lab where they are analyzed for chemical characteristics and potential toxicity to marine life.
Photo: Test chambers in the lab
Sediment and test organisms (e.g, amphipods, mussel larvae) are added to exposure chambers.
At the conclusion of the test, the organisms are evaluated for survival (amphipods) and normal development (mussel embryos).
Normal free swimming mussel embryos at only 48-hours old!
The amphipod tested (Eohaustorius estuarius)
How do we score the quality of harbor habitats?
Seafloor sediments can be used to measure habitat quality using the State of California Sediment Quality Objectives (SQOs) approach. A scoring system based on chemistry, toxicity, and biological data from each site ranks the site’s potential impact from pollutants, from Unimpacted to Clearly Impacted.
Photo: Sediment sampling in San Diego Bay
Flow chart of Integrated SQO Category determination
Integrated SQO Category score scale
Want to learn more?
Sediment quality among all four harbors combined was considered to be largely protective of healthy biota with 72% of stations classified as either unimpacted or likely unimpacted based on the SQO approach.
Want to see the full results from the 2018 RHMP?
