The San Juan Islands are part of a complex fjord estuary, with a strong saline influence from the Strait of Juan de Fuca to the south and freshwater influence from the Fraser River to the north. This archipelago, comprised of over 200 total islands, contains the larger San Juan Island, Orcas Island, Lopez Island, and Shaw Island. These closely associated islands are heavily influenced by the net influx of saline water from the Pacific Ocean, as well as a net outflow of freshwater from the Fraser River, which creates the semi-stratified estuarine environment typical for the Salish Sea (Thomson et al. 2007, Drever et al. 2023, Johannessen 2024). As water travels into the Strait of Juan de Fuca from the Pacific Ocean, it experiences coastal upwelling in San Juan Canyon, with further upwelling occurring along sills once it has traveled into the Salish Sea (Thomson et al. 2007, Alford & MacCready 2014).

Nutrients brought to the surface through upwelling support high biological productivity, with phytoplankton as the foundation of the marine food web. Some species of phytoplankton are capable of producing biotoxins, which may accumulate in marine predators, with the most severe effects on organisms which occupy a high trophic level (Lefebvre et al. 2025). In addition to wildlife mortality events, harmful algae blooms have historically impacted human health and economies in the eastern Pacific Ocean and the Salish Sea (Lewitus et al. 2012). This is especially the case in regards to shellfish species, which are capable of concentrating these toxins due to their consumption of large quantities of phytoplankton through filter feeding (Douglas et al. 1997). Continued monitoring of the physical, chemical, and biological conditions of the estuarine environment surrounding the San Juan Islands is critical to understanding how this complex, interconnected estuarine system functions, and this understanding is necessary in order to safeguard the wellbeing of both humans and wildlife in this area (Lewitus et al. 2012).

Four stations were sampled on 5/9/26 within San Juan Channel (Figures 1, 2). Stations 1 and 4 were sampled in the morning while stations 2 and 3 were sampled in the afternoon (Table 1). A zooplankton net was also conducted at stations 1 and 2.

Friday Harbor did not experience any precipitation on the day of sampling (5/9/2026). Team A (Andy, Audrey, James, Kendall, and Hozoji) sampled in the morning with Cheryl Greengrove, PhD., while Team B (Christiana, Cristian, Emily, Hannah, and Sonam) sampled in the afternoon with Julie Masura, MS.

Meteorological Information for wind speed and direction, pressure, and temperature came from NOAA Station 9449880 at Friday Harbor Labs between 5/8 and 5/9. Weather during sampling was mostly sunny with very calm waters.

Tide information is from NOAA station 9449880 at Friday Harbor Labs between 5/8 and 5/9. The tide was outgoing during the sampling of all stations.

Temperatures ranged from a low of 8.3 °C to a high of 10.2 °C, with the coldest temperatures between 60 and 108 meters of depth (Figure 5). Station 1 had the most saline water at 32.5 PSU, while other stations remained around 30 PSU (Figure 6). This aligns with CTD data collected in San Juan Channel by UW Tacoma students during previous years of sampling. Density profiles closely mirrored salinity profiles, indicating that the density of water parcels in San Juan Channel may be more influenced by dissolved solutes than by temperature (Figure 7). 

Station 1 also had an observable thermocline, halocline, and pycnocline regions around 50 meters of depth. All other stations were not as stratified, and did not display an observable thermocline, halocline, or pycnocline. Station 4 was the least stratified out of all stations, likely due to mixing as water is forced through the narrow area of Cattle Pass. Station 3 had the highest surface temperature, likely due to the influence of the outgoing tide, which could have brought waters that had been warmed in the shallow area of Friday Harbor to this station location. 

Dissolved oxygen concentrations were between 3.75 and 4.75 mL/L (Figure 8). Station 1 displayed the most range, with the highest concentration near the surface and the lowest concentration near the bottom of any station. This indicates significant stratification at this location in the Strait of Juan de Fuca. Station 4 had the narrowest range, with both near surface and near bottom concentrations just above 4.5 mL/L. This uniformity reflects the high degree of mixing present in the narrow waterway of Cattle Pass.

Fluorescence measurements were below 2.5 mg/m3  for all stations except for station 2, which peaked at 3.17 mg/m3 near the surface (Figures 9, 10). The fluorescence was equivalent to what was seen during two surveys of Commencement Bay (1, 2). This may be due to the seasonally expected spring bloom of phytoplankton having already occurred, which would explain why fluorescence was so low by the end of May. 

The CTD mounted to the rosette on the R/V Kittiwake did not have a transmissivity sensor, but did have turbidity and pH sensors (Figures 11, 12). Station 1 had the lowest turbidity, and therefore the fewest suspended particles. Turbidity at each station was very low, never exceeding 1.015 NTU. Small increases in turbidity were observed at the bottom depths of all stations, and can likely be attributed to the influence of fine seafloor sediments.

Discrete water samples were taken from Niskin bottles and processed in the lab following the UW's standard methods. Dissolved oxygen values from discrete samples were then compared to CTD measurements at the same depth. The correlation for dissolved oxygen resulted in a R2  value of 0.9487 (Figure 13). This shows a strong relationship between dissolved oxygen readings from discrete samples and those from CTD measurements, confirming that sensor equipment was functioning correctly.

Discrete chlorophyll samples were also taken from Niskin bottles and compared with CTD measurements of fluorescence from the same depths. Chlorophyll samples were processed according to the UW's standard protocol in the lab. Chlorophyll is a pigment present in photosynthetic organisms, such as phytoplankton, while fluorescence is the physical ability of that pigment to emit light; as such, the two values should be closely correlated. This comparison resulted in an R² value of 0.9478, showing a strong, positive linear relationship (Figure 14).

Station 2 had the shallowest Secchi disk depth, with light penetrating only 5 meters deep. All other stations had visibility at or beyond 6 meters of depth. The decreased visibility at station 2 may be due to its proximity to the Fraser river, as this was the northernmost station surveyed. This meant that station 2 had the greatest influence from freshwater plume of the Fraser river, a major transporter of suspended solids in this region (Johannessen 2024). These solids in the upper water column may have affected Secchi visibility at this location, and may also be the cause of the increased turbidity observed at station 2 (Figure 11).

Thalassiosira spp. was highly abundant, and was present in blooming concentrations throughout all sampling locations (Table 2).
Station 1 had the highest frequency of blooming phytoplankton species compared to all other stations, with six total blooms. Station 3 had the fewest blooming species, with only Thalassiosira spp. in bloom.

Chaetoceros socialis was blooming in all stations except for station 3 and at the Friday Harbor Labs dock (Table 2). Chaetoceros debilis was blooming only at station 1. Other members of the Chaetoceros genus not able to be identified to species were blooming at stations 1, 4, and at the Friday Harbor Labs dock.

Pseudo-nitschia spp. were categorized as blooming in station 1, which is notable as some species of Pseudo-nitschia are capable of producing a neurotoxin known as domoic acid. This can be harmful for marine predators as well as humans, especially for those who consume a diet which includes shellfish, which bioaccumulate DO through their filtration feeding strategy (Lewitus et al. 2012, Douglas et al. 1997).

A 50 meter vertical net tow for zooplankton was conducted at the stations 1 and 2, located at the North and South ends of San Juan Channel (Figure 2). Zooplankton participate in the largest mass migration on Earth, rising each night to feed on phytoplankton at the surface before descending to escape predators during the day (Haney 1988). As sampling occurred during daylight hours, vertical tows were conducted between 75 and 25 meters of depth, where zooplankton were most likely to be present. Station 2 had more total individuals than station 1, and copepods were the most abundant type of zooplankton observed at both stations (Figure 25).

Copepods are a very broad class of zooplankton, with over 15,000 described species representing 2,600 genera in more than 200 described families. These microscopic animals form an important link in the food web by consuming phytoplankton, and are then consumed themselves by larger predators such as larval fishes (Walter & Boxshall 2026).

Multiple locations throughout the channel showed stratification, especially at station 1 in the Strait of Juan De Fuca, where the influx of cold, saline water from the Pacific Ocean has the strongest presence. This is due to the increased density of these waters, which form an underlying layer, with overriding layers of less dense water (Figure 7). This stratification and influence from the Pacific Ocean explains the observable thermocline and halocline seen at station 1 (Figures 5, 6). Layers of less dense water in the upper water column are primarily supplied by the Fraser River to the north, which contributes approximately 60% of all freshwater entering the Salish Sea estuarine system (Drever et al. 2023). An overall decrease in salinity was also observed at stations 2 and 3, which were located the furthest north and therefore experienced the strongest influence from freshwater originating in the Fraser River (Figures 2, 6).

Stratification was not observed at station 4, located in Cattle Pass, due to the intense mixing that occurs when waters are forced through this narrow passageway (Figure 2, NOAA Office of Coast Survey 1991). It should be noted that even with the high uniformity observed at station 4 due to this mixing, salinity and density still remain high near the surface (Figures 6, 7). This is because station 4 is physically close to the Strait of Juan de Fuca, which brings in large amounts of dense, saline water from the Pacific Ocean (Figure 2, Thomson et al. 2007). When these parcels of waters are thoroughly mixed in Cattle Pass, the resulting water column has a uniform salinity and density that is higher than the uppermost layers observed at stations 2 and 3, as station 4 does not receive as much freshwater influence from the Fraser River (Figures 2, 6, 7). This trend toward stratification at stations with less mixing, higher salinities at southerly stations near the Strait of Juan de Fuca, and lower salinities at northerly stations near the Fraser River is typical and expected for the semi-stratified estuarine system of the Salish Sea (Banas et al. 1999).

Dissolved oxygen readings displayed similar trends in stratification based on location. Station 1 contained the highest concentration of dissolved oxygen near the surface, indicating a highly productive phytoplankton community, as the photosynthetic activity of phytoplankton increases the amount of dissolved oxygen present in water (Figure 8, Johannessen 2024). Station 1 also contained the lowest concentration of dissolved oxygen near the seafloor, where the influence of poorly oxygenated deep ocean water upwelled from the outer coast is strongest (Figures 2, 8, Alford & MacCready 2014). This extreme range, from the highest to the lowest dissolved oxygen readings of any station, supports the conclusion that the Strait of Juan de Fuca is more stratified than any other location surveyed. Station 4 was similarly the most mixed, causing Cattle Pass to have fairly uniform dissolved oxygen levels throughout the water column (Figure 8). Stations 2 and 3 displayed less thorough mixing than station 4, but also less intense stratification than station 1, which may be attributed to their location further from the Strait of Juan de Fuca and in an area with less severe bathymetric narrowing (Figure 2, NOAA Office of Coast Survey 1991). The very low dissolved oxygen concentrations recorded near the surface of station 3, and in particular the sudden drop in the uppermost 10 meters, indicates a lack of living phytoplankton. It may also point towards the presence of deceased phytoplankton, which causes oxygen consumption as decomposers perform cellular respiration (Johannessen 2024). Conversely, the higher dissolved oxygen levels present at station 2, and the sudden increase in the same area of the uppermost 10 meters, indicates the presence of living phytoplankton (Figure 8).

This conclusion is supported by fluorescence readings near the surface of station 2, which were by far the highest of any station surveyed (Figures 9, 10). This is likely caused by the high abundance of phytoplankton at this station (Figure 24). This is also a good indicator of high biological productivity in this ecosystem, as phytoplankton form the foundation of the marine food web as primary producers (Lewitus et al. 2012, Johannessen 2024). Fluorescence readings at stations 1 and 4 were similar and considerably lower than that of station 2, but showed a jump between the uppermost 5 to 25 meters (Figure 9). Since phytoplankton must remain within the upper layers of the water column in order for light to penetrate, the increase in fluorescence recorded near 25 meters of depth may be reflective of deceased phytoplankton which have sunk below surface layers, while increases in fluorescence closer to the surface may reflect living communities. Station 3 contained the lowest fluorescence readings of any station, but still displayed a similar increase between 5 and 25 meters of depth, indicating that at least some phytoplankton were present at this location (Figure 9).

The San Juan Islands may be an important area to continue surveying and monitoring efforts due to the high abundance of Pseudo-nitzschia spp. (Table 2). Approximately half of the species in the Psuedo-nitzschia genus are capable of producing domoic acid, a potent neurotoxin often abbreviated as simply "DA" (Bates et al. 1998). DA accumulates in filter-feeding shellfish, finfish, and zooplankton, causing amnesic shellfish poisoning in consumer species, which may include marine birds, mammals, and humans (Bates et al. 1998, Douglas et al. 1997, Lewitus et al. 2012). Recent modelling suggest that Psuedo-nitzschia spp. increase production of domoic acid, a secondary metabolite, as nutrients other than nitrogen become limiting. Restriction of silicate in particular was shown to result in a doubling of DA produced, with restriction in phosphorus also contributing to accelerated DA production (Moreno et al. 2022). All stations displayed lower concentrations of phosphate and silicate in surface waters when compared against samples from middle and near-bottom depths (Figures 16, 17). This reduction in the concentration of these specific nutrients near the surface is worth considering, as this upper strata of the water column is also where phytoplankton, including Pseudo-nitzschia spp., live and reproduce. Ongoing monitoring efforts may be able to detect sudden changes in nutrients at these shallow depths, which could aid in predicting harmful Pseudo-nitzschia blooms, thereby safeguarding the public against future outbreaks of amnesic shellfish poisoning.

Station 2 was found to have the most basic pH at the surface of all the sites surveyed, above 8.55 (Figure 12). The pH of seawater is naturally alkaline, as high volumes of dissolved calcium carbonate act as a massive buffer in marine ecosystems (Marion et al. 2011). The higher alkalinity observed at station 2 may also be linked to the high concentration of living phytoplankton at this site, as phytoplankton consume carbon dioxide (CO₂) during photosynthesis, thus depleting it from their surroundings. This prevents as much CO₂ from dissolving in water to form carbonic acid (H₂CO₃), which then dissociates in solution to release hydrogen (H⁺) and hydronium (H₃O⁺) ions. The opposite pattern can be seen at station 1, which had the most acidic surface waters of all sites surveyed, displaying a drop to a pH of less than 8.50 in the uppermost ten meters of the water column (Figure 12). This, combined with fluorescence data discussed above, may indicate a die-off of phytoplankton and their subsequent consumption by decomposers, which produce CO₂ through cellular respiration and therefore increase acidity (Figures 9, 12). Seeing as station 2 had a higher population of zooplankton compared to station 1, these decomposers may not be microscopic animals, but rather could represent bacterial communities (Figure 25).

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