Water Quality Monitoring

Monitoring water quality in San Elijo Lagoon Ecological Reserve


For more than 20 years, conservancy staff have conducted weekly water quality monitoring. Once a week, the water quality monitoring is conducted at six different sites in San Elijo Lagoon Ecological Reserve. The six sites, along with an ocean baseline, are shown in the map below. At each site, three measurements are taken: surface, bottom, and middle of channel. The different sites and measurements allow for the conservancy to monitor the tidal flushing of the lagoon waters and that dissolved oxygen levels can safely sustain aquatic life.

Monitoring consists of recording the tidal status and number of bays open at the inlet bridge and measuring water temperature, salinity, and dissolved oxygen. The monitoring is conducted at sunrise, before photosynthesis begins, to observe the daily lowest point of dissolved oxygen in the waters of the lagoon. By observing the daily lowest point, it makes sure the dissolved oxygen levels are not too low for aquatic life to survive. The salinity and temperatures levels show how far the tides are reaching into the lagoon and where the saltwater and freshwater are mixing. Salinity and temperature also affect how much dissolved oxygen water can hold. Cold, non-salty water can hold more oxygen than warm, salty water. As the measurements progress from the ocean to the dike east of the Interstate 5, the salinity will decrease as the ocean water meets the water of Escondido Creek.

The six locations for the weekly monitoring are at: 
W0: Ocean baseline
W1: East of Highway 101 bridge
W2: Behind Ki's Restaurant
W3: By the Nature Center
W4: Across from Cardiff Cove
W5: Underneath I-5
W6: Culvert on the dike
The two locations for the continuous monitoring are at:
SEL_NC: By Nature Center trail
SEL_Dike: Culvert on the dike
Graph of the weekly water quality measurements from the different sites.


The conservancy also collects continuous data from deployed data sensors. Currently, there is one sensor deployed near San Elijo Lagoon Nature Center and it collects a sample every 15 minutes. The sensor collects these water quality parameters: dissolved oxygen, salinity, temperature, conductivity, turbidity, chlorophyll, pH, and depth.

Conductivity – Shows what the concentration of ionic constituents is in the water. It is a good measure of total dissolved solids (TDS) and salinity in the water.

·         Temperature – Major influence on aquatic organisms because each have preferred temperatures in which they survive and reproduce. The temperature also affects water chemistry as rates of reaction increase with temperature increases. The solubility of oxygen in the water increases as temperature decreases.

     Dissolved oxygen – Important regulator of chemical processes and biological activity. Most aquatic life requires oxygen to survive. Underwater plant photosynthesis produces oxygen with adequate light. Monitoring makes sure that the lagoon waters are not becoming anoxic (depletion of oxygen) and harmful to aquatic life.

     Turbidity – Measures the clarity of the water. Shows how many particles are suspended in the water.

     Chlorophyll – Shows the activity of photosynthetic plants in the water.

Depth – Monitors the tidal height.

Salinity – Shows how much mixing is occurring of saltwater from the ocean and fresh water from the Escondido Creek.

pH– Shows the hydrogen ion concentration and whether the water is alkaline or acidic.




South of San Elijo State Beach Campground is the lagoon's only access to the Pacific Ocean. This small opening allows for fresh water and saltwater exchange. Left unattended, the inlet could remain closed much of the year from buildup of sand transported by high incoming tides and surf. Learn more.

We all need and use water. By following a few simple tips, we can save money and conserve our valuable resource. Learn more.

  A conservancy biologist deploys the continuous water sensor.

A conservancy biologist takes a depth measurement for the
weekly monitoring.


Bradley Nussbaum, Habitat Management Director
bradley [at] sanelijo [dot] org