The San Diego Bay Watersheds Common Grounds Project was created to incorporate data from water quality monitoring programs and integrate this data on a watershed level using a web-based interactive application to serve as a broad communication, education and decision-making tool; and to further develop the region's capacity to understand and assess processes affecting our water resources.

Water Quality Monitoring Training Manual
Citizen Monitoring / San Diego Coastkeeper Watershed Monitoring Program
Common Ground

Click here to download manual (PDF)


The various water quality parameters that you are going to measure, such as dissolved oxygen, conductivity, temperature, etc., serve as valuable indicators for the overall condition and health of the stream and its ability to support aquatic life and suitability for human water contact and recreation. Below is a listing of the water quality parameters you are going to measure, followed by a brief description of what they measure and why we collect them.

Water Quality Parameters

Air Temperature
Water Temperature
Dissolved Oxygen

Air Temperature

Air temperature, as you probably know, is a measure of the relative molecular motion of the gas molecules that composes our atmosphere. This motion is driven by the molecular adsorption of direct solar radiation, conduction from the earth’s surface and convection of large air masses. Faster motion results in higher temperatures, slower motion results in lower temperatures. The main constituents are nitrogen and oxygen, which compose roughly 78% and 21% of the total atmospheric gases respectively. We measure air temperature mainly to give as accurate a picture of the sampling conditions as possible, as it may help in explaining some of the following sampling results we obtain. We use degrees Celsius or Fahrenheit.


The pH is a measure of the acidity or alkalinity of a material when dissolved in water. pH is a measure of the concentration of hydrogen ions in relation to hydroxide ions. A hydrogen ion plus a hydroxide ion equals a water molecule. The pH scale ranges from 1 (lowest value, most acidic) to 14 (highest value, most basic). When both hydrogen and hydroxide ions are in equal concentration, the pH is 7 or neutral. The pH of pure dionized water is 7. Below 7, the water is acidic (there are more hydrogen ions than hydroxide ions). Above 7, the water is basic (there are more hydroxide ions than hydrogen ions). pH affects organisms’ ability to survive and reproduce, and much like temperature there are optimal ranges, usually 6.5 to 8.5. The pH of ocean water is around 8.5. pH is represented on a logarithmic, as opposed to linear, scale.


Conductivity is a measure of the ability of water to carry an electrical current. It is affected by the presence of certain inorganic dissolved solids such as chloride, nitrate, sulfate, and phosphate anions (ions that carry a negative charge) and sodium, magnesium, calcium, iron, and aluminum cations (ions that carry a positive charge). Conductivity is affected by water temperature: the warmer the water the higher the conductivity, which has to do with the solubility of ions at higher temperatures. Conductivity is measured in microsiemens per centimeter (uS/cm) with our LaMotte Tracer Pocketester.

Dissolved Oxygen

Streams gain oxygen from exchange with the atmosphere and photosynthesis, and lose oxygen from the respiration of aquatic organisms, decomposition of oxygen demanding wastes, and various chemical reactions (i.e., formation of iron oxides and other compounds).

As we see, dissolved oxygen is a balance between oxygen production and consumption. If more oxygen is being consumed than produced, aquatic organisms will likely eventually die or weaken as a result from suffocation. Dissolved oxygen concentrations below 4-mg/l are not optimal, also at lower oxygen concentrations anaerobic decomposition leads to the production of toxic compounds such as hydrogen sulfide and ammonia. Dissolved oxygen is affected by temperature: the higher the temperature, the lower the amount of dissolved oxygen. Salinity and sea surface elevation are other factors that affect dissolved oxygen. We measure dissolved oxygen in milligrams per liter (mg/L). You may also see dissolved oxygen expressed as percent saturation with is based on the solubility of oxygen at different temperatures and conductivities.


Phosphate is an essential and often limiting nutrient for aquatic plants and alga. Since phosphate is a nutrient in short supply usually, even slight increases can dramatically increase plant and algal growth (leading to algal “blooms”). For example, heavy growth of algae in streams may form dense mats on the water surface or on the stream bottom. These algal mats reduce the amount and diversity of shelter and nursery areas for small fish and aquatic invertebrates, such as mayflies and crayfish. Algae floating in the water may shade the bottom, thus reducing the growth of important submerged plants rooted on the bottom. Certain algae can also coat the leaves of the bay grasses (i.e., eel grass – Zostera marina), further reducing the amount of light that reaches these plants. Eel grass beds are essential because they provide food, shelter, and nursery areas for sea turtles, fish, blue crabs, and other marine species.

In freshwater, the decomposition byproducts of dead algae may also affect the pH of water.

When algae die (by depletion of nutrients or other factors) they settle to the bottom and are decomposed by bacteria, which consume oxygen (anaerobic decomposition). If the demand of oxygen by anaerobic decomposition exceeds oxygen re-supply the latter may lead to decreased dissolved oxygen levels and potentially to fish kills. We measure phosphate in micrograms per liter (μg/L, mg/L or ppm).


Please do not put yourself at risk to obtain a water sample.

There are several ways to safely collect a water sample. It all depends on the accessibility of the water source. When the sample source is directly accessible you can hand sample using a whirl pack bag. When the water source is below a bridge a sampling bucket can be used. A sampling pole can be used when the sample site is difficult to reach. Also, only collect a sample when the water source is flowing. If the water source is stagnant, do not collect a sample and note this in the data sheet. The following is a list of sampling techniques:

Whirl Pack Bag
Use a whirl pack bag to collect a water sample, when the water source is directly accessible. Once you are ready to collect a water sample, break the seal to the whirl pack bag and open the bag. Do not place figures into the bag. Then place the bag mid depth into water source and with one swooping motion collect the water sample. If not enough volume is collected use another whirl pack bag and transfer more water into the previous bag, or collect a new sample. You will collect the sample against the flow of the water source to allow the water to flow directly into the whirl pack bag. Once the sample is collected, seal the bag by holding the wire ends of the bag and whirling the bag in one direction and twisting the wires of the bag to form an air-tight seal.

Sample Bucket
When the water source is beneath a bridge, collect the water sample using a sampling bucket. A rope would be tied to the end of the bucket. Lower the bucket toward the water source and obtain a sample. Rinse the bucket 3 times before analysis. Analysis can be completed within the bucket but several samples will be collect in a whirl pack bag and return to Coastkeeper.

Sampling Pole
A sampling pole is used when the sampling site can not be accessed either directly or by sampling bucket. Once you have reached the sampling site and ready to sample you will wrap the wire ends of the whirl pack bag to the metal prongs of the sampling pole. Once the whirl pack bag is secure you may break the seal of the bag. You will collect the sample against the flow of the water source to allow the water to flow directly into the whirl pack bag. Once the sample is collected, unwrap the wires of the whirl pack bag and seal the bag by holding the wire ends of the bag and whirling the bag in one direction and twisting the wires of the bag to form an air tight seal.

San Diego Watershed Monitoring Instructions for Proper Use of Sampling Equipment

(Important Note: Perform tests in order listed below.)

Obtain a water sample using a whirl-pack bag, label the bag as “field sample”.

Air Temperature: LaMotte Enviro-Safe Thermometer
  1. Record instrument ID on data sheet.
  2. Place thermometer into air. Record temperature in shaded areas while standing and holding thermometer at arms length distant from your body.
  3. Allow the thermometer to stabilize with air for at least 1 minute and record temperature.
  4. Allow an additional 30 seconds between readings.
  5. Return air thermometer to whirl-pack bag dry.
Water Temperature: Fisher Scientific Traceable Termistor Thermometer
  1. Record instrument ID on data sheet.
  2. Make sure thermometer is switched to TEST and °C. Remove protective cover and switch thermometer ON.
  3. Place thermometer in water gently (as to not introduce oxygen into the sample). Do not allow thermometer to touch the bottom of water sample bag and remember to record temperature in shaded areas while standing and holding thermometer at arms length.
  4. Allow the thermometer to stabilize for at least 1 minute and record temperature.
  5. Allow an additional 30 seconds between readings (you may "freeze" reading by selecting HOLD, make sure you return to TEST mode afterwards).
  6. When finished, rinse thermometer with DI water and replace protective cover.
Dissolved Oxygen: Fisher Scientific Traceable Digital Oxygen Meter
  1. 1. Record test kit ID on data sheet.
  2. Make sure OXYGEN PROBE PLUG is connected to top of unit labeled INPUT (if necessary connect probe by properly aligning pins and pushing connector in gently).
  3. Switch unit to mg/L (DO) position and press POWER button.
  4. Immerse probe at least 10-cm into the liquid being measured. This ensures that the probe will measure the temperature of the liquid and the automatic temperature adjustment will take place. Allow 2-minutes for temperature of probe to equilibrate with liquid and for reading to stabilize.
  5. To measure the dissolved oxygen content, the velocity of the liquid being measured must be at least 0.2 to 0.3-m/s. To achieve this, immerse the probe in the solution and move it gently from side to side.
  6. Record reading.
  7. Wait 30 seconds between measurement.
  8. To hold reading, press the HOLD button, to release press HOLD button once more.
  9. After use, rinse the probe thoroughly with DI water.
pH: OAKTON Instruments pH testr 3 Double Junction
  1. Record test kit ID on data sheet.
  2. Remove cap from the electrode and press ON/OFF button to switch Testr on.
  3. Dip electrode ½ " to 1" into test solution. Stir once and wait 1-minute to let reading stabilize.
  4. To “freeze” reading press HOLD/CON button, press HOLD/CON again to release the reading.
  5. Allow an additional 30 seconds between readings.
  6. Press ON/OFF to turn off Testr, if you do not Dress a button for 8.5 minutes the Testr will automatically shut off to conserve energy.
  7. Rinse the electrode with tap water after use.
Conductivity/TDS/Salinity: LaMotte TRACER POCKETESTER
  1. Record instrument ID on data sheet.
  2. Remove cover from instrument.
  3. Turn instrument on by pressing ON I OFF button.
  4. Immerse the tester in water. The depth must be greater than or equal to 1.5 inches.
  5. Instrument is already in Conductivity Mode (μS). Don not change this mode.
  6. Wait for at least 1 minute or until reading stabilizes. Read conductivity while the probe is still in the water. Record measurement.
  7. Allow an additional 30 seconds between readings.
  8. Rinse probe with DI water and replace cover.
Phosphate: CHEMetrics Phosphate kits
  1. Record instrument ID on data sheet.
  2. Gently fill conical centrifuge tube to 25-m1 mark with sample water.
  3. Add 2 drops of A-8500 Activator Solution. Cap conical centrifuge tube and shake it in a circular motion until water becomes cloudy.
  4. Place the CHEMet ampoule in the sample cup. Break off tip of ampoule against side of sample cup and allow ampoule to fill.
  5. Wipe all liquid from exterior of ampoule. Wait 2 minutes for color development.
  6. Hold ampoule between color standards in a horizontal position and estimate concentration of sample. (To ensure consistency, have the same person estimate the concentration for all samples tested.) If the color of the CHEMet ampoule is between two color standards, a concentration estimate can be made.
  7. Dispose of ampoule and sample in appropriate hazardous waste container.
  8. Repeat Steps 2-8 a total of three times.
Salinity: REFRACTOMETER (If required)
  1. Record instrument ID on data sheet.
  2. Open cover and use dropper to cover instrument stage with sample.
  3. Close cover and point refractometer towards sun and read.
  4. To conduct additional measurements, gently shake off sample off of stage and repeat steps 2-3 a total of three times.
  5. Rinse instrument with DI water.


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