The San Juan Islands are a part of a complex fjord estuary involving the Strait of Georgia and the Strait of Juan de Fuca. The open marine waters at this intersection are well flushed as a result of strong currents, tidal mixing, and deep channels (Banas et al. 1999). There is massive circulation of freshwater within this waterway from Fraser River through the Strait of Georgia. As the freshwater travels through Haro Strait it mixes with the saltier water from the Pacific Ocean over the sills at the North and South ends of this narrow channel (Banas et al. 1999). The Haro Strait, due to its width and depth, most of the water from the tides is supplied by the strait (McLellan 2006). Previous research has found the San Juan Channel to have a well mixed water column with little stratification (Banas et al. 1999). In addition, the phytoplankton Coscinodiscus was found to be abundant during summer (Zamon 2002). 

The San Juan archipelago is comprised of over 200 islands. The four largest are Orca, San Juan, Lopez, and Shaw Island. The 2023 Estuary Field Course stayed on San Juan Island at the University of Washington's Friday Harbor Labs. San Juan has a total area of 55.39 square miles (McLellan 2006). There are no major rivers located on the San Juan Islands, with freshwater coming from small streams, precipitation, and groundwater. However the Canadian Frasier River outflow can impact the waters in this region. Run off from precipitation and potential oil spills are the major problems for the groundwater quality of San Juan (NPS 2022). On San Juan, there are no continuous streams and the lakes have no outlet that reaches the sea (McLellan 2006). 

Four stations were sampled on 5/27/23 within the San Juan Channel (Figure 1). 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 rain 5/26 or 5/27. Team B (Arthur, Eva, Mateo, Michael, Tai) sampled in the morning while some members of Team A (Clint, Gracelyn, Tim) sampled in the afternoon. 

Meteorological Information for wind speed and direction, pressure, and temperature came from NOAA at the Friday Harbor Station. The weather was warm with mild wind during the sampling period.

Tide information is from NOAA at a station located at Friday Harbor. There were no major tidal changes during the sampling period. 

Temperatures ranged from 8.5 C - 12.5 C with the coldest water along the bottom. Station 1 had the saltiest water at 32.25 PSU while the other stations remained around 30 PSU. The density profile mirrored the salinity profile which means that the density of the sea water in the San Juan channel was more determined by the salinity than the temperature. 

Stations 2 and 3 both had observable thermocline and pycnocline regions while stations 1 and 4 were less stratified. Given the small tidal changes during the sampling period, it was expected that the stations to be more stratified. 

The data for dissolved oxygen, fluorescence, and turbidity all had more noise than expected. The sensors on the CTD for these measurements might be in need of repair. 

The dissolved oxygen was between 4-5 mg/L with station 1 showing the lowest values. Given how station 1 also had the lowest temperature, the low dissolved oxygen is most likely due to the upwelling occurring in this region. 

The fluorescence was less than 2.5 mg/m3  for all stations, with the peak at station 2 at 1.6 mg/m3 . The fluorescence was equivalent to what was seen in Commencement Bay. We think the spring bloom happened already which is why the fluorescence was so low. 

The RV Kittiwake did not have a transmissivity sensor on their CTD rosette but instead had a turbidity sensor. Station 1 had the lowest turbidity. Turbidity profiled at each station was very low, never exceeding 1.015 NTU. The highest turbidity recorded was at station 4 at 117 m. Station 4 had the highest overall turbidity, while station 1 had the lowest. Small increases in turbidity were profiled at the bottom depths of the stations.

The discrete water samples taken from the bottles were processed in lab following the UW's standard methods. The discrete samples were compared to the CTD measurement at the same depth. The correlation for dissolved oxygen resulted in a R2  value of 0.89. This value shows a strong relationship between discrete samples and the CTD measurement. 

The CTD measurement of fluorescence as compared to the discrete chlorophyll measurement can be observed in the figure above. There is a very weak positive relationship between the CTD and discrete data. It should be noted that the filters were not dampened with MgCO3  before filtration of the samples, which could have affected the discrete results.

Station 2 had the lowest Secchi disk depth at 5.25 m while the rest of the stations were at or under 4 m. This means that station 2 had the clearest water on the day we sampled. 

We also converted the Secchi depth to light penetration to 1% in the water, the lowest amount phytoplankton can use. Station 2 had the deepest light penetration at 16.5 m. 

Abundance of phytoplankton was greatest at station 3 and lowest at station 4 as seen in the above concentration graph.  Station 1 has the greatest diversity of observed phytoplankton as seen in the abundance table. Chaetoceros danicus was found to be blooming at both stations 2 and 3, and abundant at station 4, making it the most frequently observed phytoplankton species.

Not shown in the figures are the phytoplankton observed in samples taken at the docks of Friday Harbor. In these dock samples, Alexandrium catenella was found. This phytoplankton causes paralytic shellfish poisoning when consumed through filter feeding shellfish. 

We conducted a zooplankton net at stations 1 and 2 which is at the North and South of the channel. Due to an meter reel reading error, the zooplankton net was conducted from 75 m to the surface as opposed to 75 m to 25 m for both stations. Amphipods were common at both stations while ecalanus and oithoma were abundant at station 1. 

The San Juan Channel shows a great change in its freshness and stratification as the water moves south through the channel. The salinity was greatest at station 1 due to the salt water coming in at the bottom from the ocean through the Strait of Juan de Fuca. Station 2 and 3 are also more stratified and fresher because freshwater is coming into the channel at the surface from the Frasier river. Due to the strength of the tidal currents within the channel, the water becomes mixed as it moves southward. 

This is a prime example of estuarine circulation as was discussed on the home page. Freshwater (less dense) coming in from the north is seen stratified in station 2 while the denser salt water is coming in from the south at the bottom at station 1. As the freshwater and saltwater move within the channel, toward stations 3 and 4, the water becomes more brackish as it mixes within the channel. This sort of circulation is also occurring within the Puget Sound. 

In addition, the dissolved oxygen and salinity profile shows a good example of upwelling. The water at station 1, which is coming from the Strait, is noticeably lower in dissolved oxygen. This is the water that, ultimately, moves into the Puget Sound. Due to the nature of this water, the Puget Sound is prone to lower oxygen conditions during times of major water stratification. 

Our results match what has previously been recorded of the water characteristics of the San Juan Channel, with it having little stratification (Banas et al. 1999). The phytoplankton Coscinodiscus was not found to be blooming or abundant at any station unlike what was found by previous researchers (Zamon 2002). Chaetoceros danicus was found at blooming abundance at stations 2 and 3. While station 2 did have the deepest light penetration, it was also very fresh at the surface which, despite having a phytoplankton bloom, it does not have a high surface abundance like station 3 does. 

The phytoplankton in the San Juan Channel was also different than what was seen in the other parts of Puget Sound during our sampling this spring. Thalassiosira was not at common or rare abundance throughout the entire channel while it was blooming at our other sampling sections. Station 1 in particular had the most unique species that we only found in the San Juan Channel. 

Master Log

README CTD File

CTD files

Secchi Data

Dissolved Oxygen

Chlorophyll

Phytoplankton Nets & Surface

Page Developed By Eva Marino and Hannah Custer