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Amateur Scientist's Guide to Water Quality Monitoring Observations


The water quality of natural waters in any region affects the drinking water in the faucet, our local food, the plants in our backyard, and the animals in nearby bodies of water and adjacent land areas.  We must protect our local water resources to ensure a healthy ecosystem around us.  But the first step in protection is to understand potential contamination of the water and its causes.  This is where water quality monitoring is required.   To solve any environmental problem, we must first understand the science behind it.  The task of an amateur scientist is to measure the water quality in your area and understand the factors that influence water quality. 

To become more involved in water quality monitoring, visit the following website:  Click on your state to see water volunteering programs in your area. 

There is not one test that measures a river’s water quality.  Our method will involve water quality monitoring, where we collect and analyze samples.  Another method is to record the abundance and diversity of organisms in the water to identify how healthy the water is for life.  The last method is to use satellite imaging rather than direct sampling for some measurements.  Each has its benefits and drawbacks: a combination and comparison of each is the most complete water quality assessment. 

Water quality is based on many factors.  They can influence the water in different ways, and the effect of each factor might be different in different locations.  Here’s a list of the main factors we will discuss that determine water quality:

Turbidity Dissolved Oxygen Temperature
Salinity pH Hydraulic Flow
Nutrients   Sources



 turbidity in river                 secchi disk



The Secchi disk is a very common way to measure the clarity of water by finding the depth at which the disk is no longer visible.  Secchi disk measurements have been performed for centuries, yet they are still a common and important oceanographic measurement on modern research cruises. 

For the best results, Secchi disk measurements should only be made on calm days between the hours of 9am – 3pm.  Measure off the shady side of the boat (or dock or pier) because sun glare can affect your reading.  Also, the same person should complete all the measurements to ensure consistency.  More than one observer can take independent Secchi disk measurements to provide a range of observational estimates.   It may also be useful to make a “viewscope” to reduce glare and aid visibility of the disk in the water.

The Secchi disk hangs at the end of a line that is marked with accurate length increments.   In deep clear waters, one-meter markings can be used.   In shallow water bodies, bays, lakes, and rivers which have more turbid water, the line may have to be marked every ten centimeters.

How to Make a Secchi Disk

Secchi Disk and Secchi Disk Viewscope

Measuring Lake Turbidity Using a Secchi Disk

secchi disk


  1. Lower the disk vertically into the water and measure the depth it disappears.
  2. Lower it a couple more feet and then pull it slowly back up.  Measure the depth it reappears. 
  3. Average the two depths for your Secchi depth.  

Related NASA Data:  K(490) is a satellite-generated image that also assesses the transparency of the water.  Compare the trend in Secchi depth to the trend in K(490.) Areas of lower Secchi depths should correspond to areas of high K(490) values. 

In addition, tests have found a mathematical relationship between these two parameters.  However, the mathematical relationship is usually specific to certain areas.  Off the coast of California, a study by Prasad and Bernstein has shown this relationship.  Studies have also been completed in the Tampa Bay.  Using the Excel Document provided, you can covert your Secchi Depth to K(490) values.  Compare this to the K(490) values in Giovanni.

Links:   Giovanni K(490), Eel River Chapter,





Salinity is an important parameter to measure in areas where fresh water meets salt water (bays and estuaries) because salinity affects oxygen in the water, water clarity, and even temperature.   Salinity is also one factor that determines the habitats where aquatic species can live.


Procedure:  The most accurate way to measure salinity is through a water salinity kit.  These cost about $20 for 6 tests.  If you are looking for a qualitative evaluation that compares the salinity of water in two locations, you can create your own low-tech salinity kit:

  1. Make .5 cm marks along an unsharpened pencil and label each.
  2. Add weight to the end of the pencil (i.e. the side with the eraser.)  A couple of thumbtacks will work as weights. 
  3. Fill a 250 mL graduated cylinder with fresh water.
  4. Place the pencil in the water with the eraser face down. 
  5. Adjust the weights as needed.
  6. Record the height of the pencil
  7. Now fill with two salt water samples and compare. 

(adapted from the Eyes on the Bay Lesson Plan:

A pencil that floats higher will be more salty because salt water is denser and can, therefore, support more mass.

salinity map


Related NASA datasets:  Above is a map of average salinity values across the globe.  In many cases, the salinity will correlate with temperature data.  See how temperature compares to salinity by looking at Sea Surface Temperature Data (MODIS) on Giovani.

Links:   Giovanni SST, Chesapeake Bay Chapter,




global sea surface temperature


Many chemical and biological processes in water depend on temperature.  For example, some fish can only live and reproduce in a certain temperature range.  In contrast, some diseases thrive in certain temperatures and can spread easily if that temperature is reached.  In the Chesapeake Bay during the summer, the location of stinging jellyfish called “sea nettles” can be predicted based on the temperature of the water. 

Below is a chart of optimal temperatures for certain fish: 

Species Max. Weekly Average Temp. for Growth (Juveniles) Max. Temp for Survival of short exposure (juveniles) Max. weekly average temp. for spawning Max. temp. for embryo spawning
Atlantic salmon 20C(68F) 23C(73F) 5C(41F) 11C(52F)
Bluegill 32C(90F) 35C(95F) 25C(77F) 34C(93F)
Brook Trout 19C(66F) 24C(75F) 9C(48F) 13C(55F)
Common Carp --- --- 21C(70F) 33C(91F)
Channel catfish 32C(90F) 35C(95F) 27C(81F) 29C(84F)
Largemouth bass 32C(90F) 34C(93F) 21C(70F) 27C(81F)
Rainbow Trout 19C(66F) 24C(75F) 9C(48F) 13C(55F)
Smallmouth Bass 29C(84F) --- 17C(63F) 23C(73F)
Sockeye Salmon 18C(64F) 22C(72F) 10C(50F) 13C(55F)

(Brungs and Jones: 1977,

Procedure:   Just as a thermometer can measure your own temperature, it can also be used to measure the temperature of water.  However, water temperature varies based on location in the water and depth.  For example, a spot under the shade at a low depth could be significantly cooler than one close to the surface in the sun.  Make sure to take a variety of samples across the water and vary the timing of the samples throughout the day.    


Note that if consistent and reliable water temperature measurements are desired, a calibrated thermometer is required.   Modern digital thermometers can be self-calibrated.  Submersible thermometers can be used to measure the temperature profile of a body of water.   In many water bodies, a thermocline (the boundary between deeper cold water and warm water at the surface) develops in the spring and summer, and it can be very shallow, sometimes only a meter or so below the surface.   Submersible thermometers can be lowered to specific depths – the marked line for the Secchi disk can be used – and a temperature profile can be measured.   Remember that the thermometer will have to stay at a specific depth for a few minutes to properly measure the depth of the water, and the temperature reading will start to change as soon as warmer temperatures are encountered.


Related NASA data:  The Sea Surface Temperature (MODIS) Satellite measures temperature across the ocean.  Compare your results to satellite imagery. 

Links:   Giovanni SST, Benguela Upwelling Chapter,



Dissolved Oxygen


Dissolved Oxygen (DO) is one of the most important criteria for water quality testing.  It measures the amount of oxygen in the water, which all organisms use to breathe.  Low oxygen levels can seriously impair animal growth and impact the survival of aquatic organisms.  The air we breathe contains about 21% oxygen.  Water has significantly less than that, ranging from 0-18 parts per million (ppm) – or .0018%.  Normal values are 5-6 ppm to support a healthy population.  Dissolved Oxygen can not be easily predicted or determined because it depends on many factors including temperature, wind, chlorophyll concentrations, and nutrients.  Here is a chart from the EPA Chesapeake Bay Program that outlines the factors and their effects:

diagram of effects of DO



As you can see in the diagram above, temperature affects dissolved oxygen.  Colder water can hold more dissolved oxygen than warm water because warm water contains faster moving molecules that ‘knock’ the oxygen molecules back into the air.  Here is a chart outlining the maximum dissolved oxygen concentrations given the temperature of the water measured by the EPA: 

dissolved oxygen maximums versus temperature


Procedure:   The easiest and most efficient way to measure dissolved oxygen is using a probe.  Kits also contain ways to measure dissolved oxygen.  The Azide-Winkler Method is the most accurate, but it requires strong chemicals and the most training.  Here’s a link to the EPA guidelines for the accurate method for DO testing:,

Related NASA data:Although there is no satellite imagery of oxygen levels of the ocean, oftentimes we can correlate low dissolved oxygen levels with high chlorophyll levels.  When phytoplankton die and this dead organic matter sinks to the bottom, bacteria consume the matter in a process that depletes oxygen from the water.   Hypoxia – or loss of oxygen – occurs, a process called “eutrophication”.  Without oxygen, no organisms can survive in the deeper waters, leaving only phytoplankton to thrive on the surface.  Algae blooms, or plumes of phytoplankton, are indicators of hypoxia. These algae blooms can be monitored through chlorophyll data from satellites.  Compare chlorophyll a concentrations with DO measurements from the field.  Also, look at the temperature data in Giovanni to see how temperature affects DO. 

Links:   Giovanni SST and chlorophyll a, Long Island Sound Chapter,,





The pH of water, signified by the acidity of the water, measures the amount of hydrogen in the water.  Low pH (high acidity) means that there are more hydrogen atoms in the water whereas high pH (high alkalinity) means there are less hydrogen atoms available in the water.    Normal pH in the Chesapeake Bay ranges from ph 7 to pH 9.  Higher pH is usually associated with higher levels of chlorophyll and algae blooms. 

The most serious effects of pH on water quality are found where the underlying geology does not provide sufficient dissolved minerals for the water to neutralize (“buffer”) acidic input, either from acid rain or runoff, especially in mining regions.    In these areas, streams and lakes can become increasingly acidic, which has detrimental effects on aquatic life.

pH scale



Here’s a list of conditions associated with different pH values laid out by the Kentucky Water Watch Program: 

Min Max Effects
3.8 10.0 Fish eggs could be hatched, but deformed young are often produced
4.0 10.1 Limits for the most resistant fish species
4.1 9.5 Range tolerated by trout
--- 4.3 Carp die in five days
4.5 9.0 Trout eggs and larvae develop normally
4.6 9.5 Limits for perch
--- 5.0 Limits for stickleback fish
5.0 9.0 Tolerabe range for most fish
--- 8.7 Upper limit for good fishing waters
5.4 11.4 Fish avoid waters beyond these limits
6.0 7.2 Optimum (best) range for fish eggs
--- 1.0 Mosquito larvae are destroyed at this pH value
3.3 4.7 Mosquito larvae live within this range
7.5 8.4 Best range for growth of algae


Using this chart, you can identify whether the fish in your area can survive in the pH range you found in your water.

Procedure:  The two tests for pH are litmus paper, which can be found in a water quality kit, or probes.  The values will range from 0 – 14.  

Related NASA data:  The satellite-generated chlorophyll concentrations can show some correlation.  As stated above, higher pH is correlated with higher levels of chlorophyll. 

Links:   Giovanni Chlorophyll a, Gulf Stream Chapter,,




picture of red algae bloom 


The two most important nutrients for aquatic plant growth are nitrogen and phosphorous.  Increases in either can lead to blooms of algae.  Blooms of algae are a rapid, excessive growth of algae that can block sunlight to the organisms underneath the water.  In addition, bacteria consume the dead organic matter generated by phytoplankton growth and death in a process that depletes oxygen from the water.  Without dissolved oxygen, larger organisms and bottom-dwelling (“benthic”) organisms can’t survive in deeper waters.  Nutrients, therefore, affect chlorophyll concentrations, dissolved oxygen, and other water quality indicators through this process.  This diagram from the Eyes on the Bay Program run by the Department of Maryland’s Natural Resources outlines the process:

flow chart of interaction between nutrients and other water parameters


Procedure:   Nitrogen and phosphorous samples can be determined from a water quality kit or analyzed by a professional in the lab.  Kits can cost anywhere from $20 - $100, depending on the level of accuracy needed and the number of tests included.  For an amateur scientist, these kits are your best bet.  However, with the help of a teacher or lab technician, you could also run more accurate samples in the lab.  The EPA has guidelines for testing phosphorous and nitrates (as well as other parameters) on its website:

Related NASA data:   As mentioned earlier, nutrient concentration affects chlorophyll concentration.  Compare the satellite-generated chlorophyll data to your nutrient samples collected in the field. 

Also remember that streams and rivers contribute nutrients to bays and estuaries, and ultimately to the ocean.   So monitoring local streams for nutrient concentrations can discover nutrient “hot spots” (perhaps where a golf course is using too much fertilizer).  So local streamwater monitoring can allow environmental agencies to improve water quality in streams, rivers, lakes, and along the coast.

Links:   Giovanni Chlorophyll a, Eel River Chapter,,



Hydraulic Flow


Measuring water flow is important to understand the concentration of nutrients from rivers and streams and the total nutrients entering the area.  River and stream discharge is the primary way that nutrients are transported.   Excess nutrients can contribute to the variety of water quality problems discussed earlier in the chapter.

picture of river flow


Important safety note:   Working near flowing rivers and streams can be dangerous.  If measurements such as these are being considered, the area being measured should be easily accessible and free of hazards both on land and in the water.   Stream measurements should always be done in teams, not by individuals.   Be aware of the dangers of swiftly-flowing water and the possibility of flash floods.

Procedure:  Using a flowmeter or propeller to measure water flow is the most accurate method.  However, these devices can be expensive, $300-500.  Instead, you can follow the low-tech alternative below.  If you have access to a propeller, you can follow the instructions on ‘A Citizen’s Guide to Understanding and Monitoring Lakes and Streams:



  1. Make two transects across the river that are 20 meters apart.  Note: the stream area needs to be straight and fast-moving with riffles and runs.  It should not contain slow areas such as pools.
  2. Set up stakes on either side of the river with string attached between at the upstream and downstream location as shown below:


  1. Divide the width into four equal sections.  Mark these sections with string or markers. 
  2.  Measure the depth at each of the four sections.
  3. Average the depth calculations: add the three depth calculations for each transect and divide by 4. (to account for 0 depth at the shoreline)
  4. Multiply the average depth by the width of the transect.  Now, you have the average area for each transect. 
  5. Average the two transect areas: add the two areas and divide by 2.  This gives you the average area of the river.    


  1. Now, find the fastest flowing part of the river. 
  2. Place an orange in the current and measure the time it takes to reach the downstream transect.  Note: an orange is good to use because its natural buoyancy allows it to flow in the fastest depth (.6 of the depth of the river.)
  3. Use the total discharge calculation above to find the total discharge. 

velocity(m/s) * total area(m2) = total discharge (m3/s)

  1. Make sure to have a fishing net to scoop the orange out at the end!

Go to the EPA chapter to see more detailed instructions:

Related Datasets: You can compare your findings to government flow estimates of select rivers at the website:  Also, look at K(490) to see how turbidity relates to the discharge.       


Links:   Giovanni K(490) and Chlorophyll a, Mississippi River Chapter,,,   




pollution diagram 


In order to change water quality conditions, we must understand what is causing the harmful conditions in the first place.  After determining the health of the water in your area, try to predict the origin of each effect.  Here is a chart of possible contamination sources:

Source Commonly Associated Chemicals Found
Cropland Turbidity, phosphorous, nitrates, temperature, total solids
Forestry harvest Turbidity, temperature, total solids
Grazing land Fecal bacteria, turbidity, phosphorous, nitrates, temperature
Industrial discharge Temperature, conductivity, phosphorous, nitrates, temperature
Mining pH, alkalinity, total dissolved solids
Septic systems Fecal bacteria (i.e., Escherichia coli, enterococcis), nitrates, phosphorous, dissolved oxygen/biochemical oxygen deman, conductivity, temperature
Sewage treatment plants Dissolved oxygen and biochemical oxygen demand, turbidity, conductivity, phosphorous, nitrates, fecal bacteria, temperature, total solids, pH
Construction Turbidity, temperature, dissolved oxygen and biochemical oxygen demand, total solids, and toxics
Urban Runoff Turbidity, phosphorous, nitrates, temperature, conductivity, dissolved oxygen and biochemical oxygen demand.


Related NASA data:   Look at NASA data at the website:  Under Land, choose Land Cover Classification.  Look at the land type classifications and zoom in to your area.  Also, check out Google Earth images to see land types near you.

NEO image






Volunteer Monitoring Websites:

EPA Volunteer Stream Monitoring: A Methods Manual:

A Citizen’s Guide to Understanding and Monitoring Lakes and Streams:

List of Water Quality Monitoring Programs by State:!OpenView&Start=30&Count=30&Collapse=30#30

Kentucky Water Watch:

Water Quality Data:

USGS Streamflow Conditions across US:

Eyes on the Bay:

Long Island Sound Study:

Satellite Data:

Giovanni Ocean Color:

Giovanni-NEO Instructional Cookbook:


Google Earth or Google Maps:

NASA Aquaris Mission(Salinity):



Prasad, K.S., Bernstein R.L., Kahru, M., and Mitchell, B.G. “Ocean Color Algorithms for Estimating Water Clarity (Secchi Depth) from SeaWiFS” Scripps Institution of Oceanography, San Diego CA. 1999.

Chen, Zhiqiang, Muller-Karger, E., Hu, Chuanmin. “Remote sensing of water clarity in Tampa Bay,” Institute for Marine Remote Sensing, University of South Florida. 2007. 

Acker, J. G. & Leptoukh, G. (2007).  “Online analysis enhances use of NASA earth science data.”  Eos, Trans., Amer. Geophysical Union, 88 (2), 14, 17.

Click here for a list of publications on theGiovanni site. 


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Last updated: Apr 06, 2016 10:25 AM ET