Biological Sciences, Santa Barbara City College pipeline center for sustainability

Biology 130: Methods in Field Biology

Field Technique:  Stream Habitat Assessment (Physical Characterization/ Water Quality)

HABITAT ASSESSMENT AND PHYSICOCHEMICAL PARAMETERS (From Rapid Bioassessment Protocols For Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates, and Fish Second Edition)

An evaluation of habitat quality is critical to any assessment of ecological integrity and should be performed at each site at the time of the biological sampling. In general, habitat and biological diversity in rivers are closely linked (Raven et al. 1998). In the truest sense, “habitat” incorporates all aspects of physical and chemical constituents along with the biotic interactions. In these protocols, the definition of “habitat” is narrowed to the quality of the instream and riparian habitat that influences the structure and function of the aquatic community in a stream. The presence of an altered habitat structure is considered one of the major stressors of aquatic systems (Karr et al. 1986). The presence of a degraded habitat can sometimes obscure investigations on the effects of toxicity and/or pollution. The assessments performed by many water resource agencies include a general description of the site, a physical characterization and water quality assessment, and a visual assessment of instream and riparian habitat quality. Some states (e.g., Idaho DEQ and Illinois EPA) include quantitative measurements of physical parameters in their habitat assessment. Together these data provide an integrated picture of several of the factors influencing the biological condition of a stream system. These assessments are not as comprehensive as needed to adequately identify all causes of impact. However, additional investigation into hydrological modification of water courses and drainage patterns can be conducted, once impairment is noted.

The habitat quality evaluation can be accomplished by characterizing selected physicochemical parameters in conjunction with a systematic assessment of physical structure. Through this approach, key features can be rated or scored to provide a useful assessment of habitat quality.


Both physical characteristics and water quality parameters are pertinent to characterization of the stream habitat. The information required includes measurements of physical characterization and water quality made routinely to supplement biological surveys.

Physical characterization includes documentation of general land use, description of the stream origin and type, summary of the riparian vegetation features, and measurements of instream parameters such as width, depth, flow, and substrate. The water quality discussed in these protocols are in situ measurements of standard parameters that can be taken with a water quality instrument. These are generally instantaneous measurements taken at the time of the survey. Measurements of certain parameters, such as temperature, dissolved oxygen, and turbidity, can be taken over a diurnal cycle and will require instrumentation that can be left in place for extended periods or collects water samples at periodic intervals for measurement. In addition, water samples may be desired to be collected for selected chemical analysis. These chemical samples are transported to an analytical laboratory for processing. The combination of this information (physical characterization and water quality) will provide insight as to the ability of the stream to support a healthy aquatic community, and to the presence of chemical and non-chemical stressors to the stream ecosystem. Information requested in this section (Appendix A-1, Form 1) is standard to many aquatic studies and allows for some comparison among sites. Additionally, conditions that may significantly affect aquatic biota are documented.

Habitat Assessment Data Sheet (High Gradient- Single Habitat Approach)

Habitat Assessment Data Sheet (Low Gradient- Multiple Habitat Approach)

Details on filling out the Habitat Assessment Data Sheet

Views of parts of the streamside forests:

Habitat Assessment (Physical Characterization/ Water Quality) Data Sheet



Physical Characteristics and Water Quality (much of the following is from Santa Barbara Channel Keeper)

The following are measurements that can be done relatively quickly and indicate several important physical and chemical endpoints. Each one looks at a parameter that directly or indirectly impacts water quality and the health of the aquatic biological community.



The trees and other vegetation that overhang the water provide shade that keep water cooler.

riparian shade
(The riparian zone in this area is dominated by fast growing trees with relatively large leaves like Western Sycamore and White Alder. This canopy creates significant shade and keeps water in the creeks cool. You will also generally find boulders and fallen limbs in the creeks which create micr-habitat for invertebrates, hiding places for small fish, and riffles where water bubbles and adds dissolved oxygen. Photos by Adam Green)

Water temperature directly affects biological and chemical processes. Some fish species, such as steelhead trout, prefer colder water, others prefer warmer water.

For example, trout need temperatures lower than 19 °C (66 °F) to do well and lower than 9 °C (48 °F) to spawn, but can stand temperatures as high as 24 °C (75 °F) for short periods.

For catfish, these limits are 32 °C (90 °F), 27 °C (81 °F) and 35 °C (95 °F).

Water temperature affects the oxygen content of water – the higher the temperature, the less oxygen it can hold. Fish and benthic macro-invertebrates will move around within the stream to find their optimal temperature.

In the figure to the left you can see that different life stages also have optimal temperatures as indicated by the boxes.

water temps for steelhead in truckee river


Temperature can also be affected by many human activities. Examples include:

• Building dams or artificial stream channels alters the flow rate, which in turn can affect temperature.
• Removing streamside vegetation reduces shade which would normally keep the water cool.
• Construction or other human activities near streams can increase sedimentation, which traps more heat in the water.
• Water effluent from industrial sources such as power plants can drastically change water temperatures.


Canopy Coverage:

Describing a creek as "shady" is not sufficient to conduct scientific research. We need to be able to quantify the canopy coverage and the "shadyness." This way we can see if other factors correlate with these data, how canopy coverage affect ecosystem health, and what changes occur throughout a year or after a disturbance.

For example, the El Nino storms in 2016 have caused several trees to fall in the rattlesnake canyon creek area.

tree fall at rattlesnake canyon


This will certainly increase sun exposure during the middle of the day, but by how much. How much of an impact will this have on water temperature, dissolved oxygen, invertebrate diversity etc.?

Shade can have direct and indirect effects on species composition insode and outside the creek. For example, Shade may mitigate invasive plant presence, richness

There are a few ways to quantify canopy coverage. The spherical densiometer is one of the more accurate methods.

Use of a spherical densiometer:

Take four densiometer readings from the center of each transect while facing north, south, east and west.  Average these four readings.  

Facing up stream, keep the instrument leveled (indicated by the round level in the lower right-hand corner).  Hold the densiometer far enough away from your body so that your head is just outside the grid (12-18” away). Maintain the densiometer approximately 1 foot above the water.

There are a total of 24, 1/8” x 1/8” squares in the grid.  Each square represents an area of canopy opening (sky image or unfilled squares) or canopy cover (vegetation image or filled squares).  Count the number of canopy opening squares.  If there are squares that are only partially filled, these can be added to make a complete square.   

The uncovered area is determined by multiplying the number of squares by 4.17.  Subtract this number from 100% to determine overstory density in %.   e.g.  100% - (10 unfilled squares x 4.17) = 58.3% overstory density


spherical densiometer


If more than half of the canopy area is open sky the counting process can be reversed. Count the filled square areas that are covered by the canopy. Multiply by 4.17 to obtain the estimated overstory density directly in percent. (i.e.  Number of filled squares x 4.17 = % overstory density)  

In the image above, the numbers indicate amount filled. The 2 squares on the right include area filled by a nearby building, so I considered the building open space.


Dissolved Oxygen (DO):

Aquatic organisms rely on the presence of oxygen in streams; not enough oxygen and they will move, weaken or die. In water, oxygen is a dissolved gas. Water temperature, altitude, time of day, and season can all affect the amount of oxygen in the water; water holds less oxygen at warmer temperatures and high altitudes. DO is measured either in milligrams per liter (mg/L) or “percent saturation.” Milligrams per liter is the amount of oxygen in a liter of water. Percent saturation is the amount of oxygen in a liter of water relative to the total amount of oxygen that the water can hold at that temperature.

As dissolved oxygen levels in water drop below 5 mg/L, aquatic life is put under stress. Colder water fish (trout) need levels above 6, and DO above 7 mg/L may be required for spawning. Warm water fish can probably tolerate levels as low as 4. The lower the concentration, the greater the stress. Oxygen levels that remain below 1-2 mg/l for a few hours can result in large fish kills.

Oxygen is both produced and consumed in a stream. Because of constant churning, running water dissolves more oxygen in a stream than the still water found in pools.


(The rush of water over boulders and other debris pushes oxygen into the water. Photo by Adam Green)


Aquatic plants and algae affect dissolved oxygen concentrations by releasing oxygen underwater during photosynthesis – DO is at a maximum in the late afternoon of a sunny day. Throughout the night, the same plants and algae, joined by the other aquatic organisms, remove oxygen through respiration, reducing levels of DO to their lowest by early morning. Early mornings, during periods of hot weather and low flows, are the best time to determine whether DO is declining to dangerous levels.



While both phosphorus and nitrogen are essential nutrients for plants and animals that make up the aquatic food web (nitrogen for protein synthesis and phosphorus for energy transformation in cells), in excess amounts they can cause severe problems. Plants and soil micro-organisms take up these nutrients in run-off because they use the nutrients for themselves. The riparian vegetation slows water entering the aquatic system allowing more of the water to sink into the soil and allowing the plants and soil organisms to take up these nutrients.

Since phosphorus is the nutrient in short supply in most fresh waters, even a modest increase in phosphorus can, under the right conditions, set off a whole chain of undesirable events in a stream including accelerated plant growth, algae blooms, low dissolved oxygen, and the death of certain fish, invertebrates, and other aquatic animals. This over-fertilization is called eutrophication.

There are many sources of phosphorus in water, both natural and human. These include

  • soil and rocks,
  • animal and plant waste,
  • wastewater treatment plants,
  • runoff from fertilized lawns and cropland,
  • failing septic systems,
  • runoff from animal manure,
  • disturbed land areas and drained wetlands.

We also see an influx of these nutrients after a fire when large amounts of vegetation have been burned releasing the nitrogen and phosphorous that can wash into aquatic systems with the next rain. More recently, fire retardants made with phosphorous used to suppress and fight wildfires have contributed a large amount of this nutrient to aquatic systems.

Phosphorus in water comes in many forms. Both organic and inorganic phosphorus can either be dissolved in the water or suspended (attached to particles in the water column).

Nitrogen is also found in the water column in different forms: as dissolved inorganic nitrogen (nitrate, nitrite and ammonium) and as dissolved or suspended organic nitrogen (complex molecules associated with living, or once living, tissue). Nitrates are the most common form of nitrogen found in our local streams. Together with phosphorus, nitrates in excess amounts can accelerate eutrophication, causing dramatic increases in aquatic plant growth and changes in the types of plants and animals that live in the stream. This, in turn, affects dissolved oxygen, temperature, and other indicators.

Excess nitrates can become toxic to warm-blooded animals, particularly babies, at higher concentrations (greater than 10 mg/L) and may also be cancer causing. Sources of nitrates include

  • wastewater treatment plants,
  • runoff from fertilized lawns and cropland,
  • failing on-site septic systems,
  • runoff from animal manure, and
  • industrial discharges

Nitrates end up in rivers and streams more quickly than other contaminants like phosphorus, because they dissolve in water more readily and are not adsorbed on soil particles.

Channelkeeper samples are analyzed at UCSB for nitrate, dissolved organic nitrogen, phosphate and suspended organic nitrogen and phosphorus.

Cultural Eutrophication is when humans add limiting nutrients to an aquatic system. The limiting nutrients of Nitrogen and Phosphorus allow native algae populations to grow much larger.


(Two creeks with large algal blooms fed from nutrients in the creek)


(The above graph shows the change in Dissolved Oxygen throughout the day in the creek in the image above right)


Aquatic systems with large populations of algae can show large swings in DO levels throughout a 24 hour period, with super saturated DO levels during the day when algae are producing O2 from photosynthesis and very low levels of DO at night.

If aquatic plants and other organisms die, then decomposers (i.e. bacteria) use up O2 as they go through their own metabolism consuming the dead organisms. Their populations increase further decreasing O2 in the water. Algae will eventually die as they outgrow their carrying capacity adding more food to decomposers.

In a low O2 environment many bacteria will switch to anaerobic metabolism or different anaerobic species will become dominant and release CH4 (methane) and H2S (Hydrogen sulfide- rotten egg smell) that are poisonous to many species- and stink. Most species that can move will. Fish deaths can occur in severe cases. 

With higher levels of Hydrogen Sulfide, sulfur eating bacteria can proliferate. These bacteria are pink and can cause the water to turn and odd pink color.


pink sulfur eating bacteria in bird refuge
(The Santa Barbara bird refuge next to the Zoo after a eutrophication event. First, the refuge became very stinky due to the Hydrogen sulfide, then the smell went away and the water turned pink as the sulfur eating bacteria fed on the sulfide and proliferated. Photo by Adam Green)


Additionally, because algae are taking CO2 out of the water they can actually increase pH. In water, CO2 forms H2CO3 (Carbonic Acid). As algae take the CO2 out of the water it causes a decrease in the H2CO3 and a decrease in acidity (an increase in pH).



pH is a relative measure of alkalinity and acidity, it’s an expression of the number of free hydrogen atoms present. It’s measured on a scale of 1 to 14, with 7 indicating neutral – neither acid nor base. Lower numbers show increasing acidity, whereas higher numbers indicate more alkaline waters. Blood (pH of 7.5), seawater (9.3) and household ammonia (11.4) are all alkaline or basic; urine (6), oranges (4.5), Coca Cola Classic (2.5) and the contents of your stomach (2) are acidic. pH numbers represent a logarithmic scale so small differences in numbers can be significant: a pH of 4 is a hundred times more acidic than a pH of 6. Most species of life have a specific pH range in which they can survive. A wide variety of aquatic animals prefer a range of 6.5-8.0 pH. If pH is altered beyond an organism’s normal range it will suffer and soon die off. Many pollutants push pH readings toward the extremes of the scale. A change of more than two points on the scale can kill many species of fish.




Low pH can also allow toxic elements and compounds to become mobile and “available” for uptake by aquatic plants and animals.



Turbidity is a measure of water clarity. Turbidity is affected by suspended particles, or solids that cannot dissolve, including clay, silt, sand, algae, and plankton. Natural factors like wave action, changes in seasonal light intensity, and erosion, can all alter turbidity. However, turbidity is often increased by human activities. Clear cut logging, construction, and mining all greatly increase unnatural soil erosion which rapidly changes turbidity. Regular monitoring of turbidity can help detect trends that might indicate increasing erosion from these activities. Changes in turbidity can have dramatic impacts on the aquatic ecosystem.

Examples include:

• Suspended sediments trap heat, raising the temperature of the water and decreasing the amount of oxygen it can hold.
• When turbidity levels are high, less light passes through the water, and photosynthesis slows, decreasing oxygen levels and primary productivity.
• Water that is highly turbid can clog the gills of fish and bury their eggs.


Vegetation slows water movement, allowing water to sink into the ground and decreases erosive force. The root systems of the vegetation are like rebar in a building that stabilizes the bank decreasing erosion.


stream bank with roots(Roots holding side of creek bank, Rattlesnake Canyon, Santa Barbara, CA. Photos by Adam Green)

Less erosion means less sediment in the creek. When there is more sediment in the creek it can make it difficult for aquatic species to see, breathe, and reproduce (silt can cover eggs and decrease O2 to eggs).



Water is one of the most efficient solvents in the natural world and has the ability to dissolve a great many solids. Many of these solids carry an electrical charge when put into solution. For example, chloride, nitrate, and sulfate carry negative charges, while sodium, magnesium, and calcium have a positive charge. These dissolved substances increase water’s conductivity – its ability to conduct electricity. Therefore, measuring the conductivity of water indirectly indicates the amount total dissolved solids (TDS). It’s not a perfect measure because some substances, particularly organic compounds like oil, alcohol or sugar do not conduct electricity well and have low conductivity, but conductivity is a rough approximation of TDS.

Each stream tends to have a relatively constant range of conductivity that, once established, can be used as a baseline for comparison with regular conductivity measurements. Significant changes in conductivity could then be an indicator that a discharge or some other source of pollution has entered a stream. Conductivity tends to decrease in the winter when heavy rainfall and runoff increase the amount of fresh water flow. With more water, mineral concentrations are more dilute. On the other hand, in late summer and fall, especially during periods of drought, the dissolved solids are more concentrated, raising conductivity. Conductivity is also affected by temperature: the warmer the water, the higher the conductivity. For this reason, conductivity is reported as conductivity at 25 degrees Celsius (25 °C).

The basic unit of measurement is the siemen. Conductivity is measured in micro-siemens per centimeter (µs/cm) or milli-siemens per centimeter (ms/cm). Distilled water has a conductivity in the range of 0.5 to 3 µs/cm. The conductivity of rivers in the United States generally ranges from 50 to 1500 µs/cm. Drinking water usually has to meet a standard of 500 mg/L TDS – a conductivity of roughly 1000 µs/cm. Conductivity in Santa Barbara and Ventura streams is usually above 1000 µs/cm because of high mineral content in the easily eroded sediments that form our coastal mountains.




water flow
(Creek flow. Photo by Adam Green)


Stream flow is the volume of water that moves past a fixed point during a specific interval of time. Flow is generally measured in cubic feet per second (cfs) – the number of cubic feet of water moving down the stream channel in one second. Think of it as the width of the stream at some point, times its average depth times its average velocity: (width in feet) x (depth in feet) x (velocity in feet per second) = flow in cubic feet per second. Knowing the flow is critical in calculating the amount of a contaminant in a stream. When we test for bacteria, nutrients, or total dissolved solids, we only determine the concentration in the water. Once we measure flow we can we quantify the actual amount being carried through the system (the amount is equal to the flow multiplied by concentration).

Flow affects water quality in a variety of ways:

  • Flow influences the ability of a stream to dilute pollution; large, swift rivers have a greater ability to dilute pollution than smaller streams.

  • Flow and velocity affect the available oxygen level in water: higher velocities and flows generate higher levels of turbulence which in turn, cause more air to be mixed within the flow. Streams with higher flows generally have more oxygen available for aquatic organisms.

  • Flow controls the amount of sediment that is transported in a stream. Streams with higher velocities and larger flows can transport greater amounts of sediment

Calculating volume of water discharged from the creek requires measurement of cross sectional area. Data on creek width and depth along with corresponding flow rate can be entered into this spreadsheet to calculate discharge.


Bacteria: Total Coliform, E.Coli, and Enterococcus

Members of two bacteria groups, coliforms and fecal streptococci, are used as indicators of possible sewage contamination because they are commonly found in human and animal feces. Although they are generally not harmful themselves, they indicate the possible presence of pathogenic (disease-causing) bacteria, viruses, and protozoans that also live in human and animal digestive systems. Therefore, their presence in streams suggests that pathogenic microorganisms might also be present and that swimming and eating shellfish might be a health risk. Since it is difficult, time-consuming, and expensive to test directly for the presence of a large variety of pathogens, water is usually tested for coliforms and fecal streptococci instead. Sources of fecal contamination to surface waters include wastewater treatment plants, on-site septic systems, domestic and wild animal manure, and storm runoff.

Stream Team collects samples that are brought back to the Channelkeeper lab and analyzed for three types of bacteria:

  • Total Coliform: Total coliforms are a widespread group of bacteria in nature. All members of the total coliform group can occur in human feces, but some can also be present in animal manure, soil, vegetation and submerged wood and in other places outside the human body. Thus, the usefulness of total coliforms as an indicator of fecal contamination depends on the extent to which the bacteria found are fecal and human. For recreational waters, total coliforms are no longer recommended as an indicator, but they are still the standard test for drinking water because their presence indicates contamination of a water supply by an outside source.

  • E. coli: E. coli is a species of fecal coliform bacteria that is specific to fecal material from humans and other warm-blooded animals. EPA recommends E. coli as the best indicator of health risk from water contact in recreational waters.

  • Enterococcus: Enterococci are a subgroup of the fecal streptococci bacteria, and are typically more human-specific. Enterococci are distinguished by their ability to survive in salt water, and in this respect they more closely mimic many pathogens than the other indicators. The EPA recommends enterococci as the best indicator of health risk in salt water used for recreation and as a useful indicator in fresh water as well.



Bacteria are reported as the “most probable number” (MPN) of bacteria in 100 milliliters (100 ml, about 4 ounces) of water; we use a statistical test instead of directly counting bacteria so the actual number is an estimate. California Public Health requirements for bacteria counts are complicated and vary somewhat by jurisdiction; what follows is simply a broad outline.

There are two limits for each test, a single sample limit and a limit for an average of 5 or more weekly samples.

For recreational use, the total coliform limits are "no more than 10,000 per 100 ml in a single sample, and an average of less than 1000." For E. coli the "average" limit is 126 bacteria/100 ml of water and the single sample limit varies from 235 to 500 depending on intensity of use (235 for beach areas, 500 for occasional use). For enterococcus the "average of 5 or more samples" limit is 35 and the single sample limit is 104 (there is general agreement on the 35 limit, but various jurisdictions in the state vary the single sample limit between 104 and 500).

Plate of Coliform Bacteria


The image of a petri dish showing bacterial colonies from a water sample is not the exact way it is done with Channel Keeper, but it shows a method for determining presence and an estimate of concentration of bacteria. In the image water was placed on the petri dish and incubated allowing the bacterial colonies to grow large enough to be seen and counted. I circled the colonies for counting. The photo was taken some time after I completed the count so more colonoies appeared, but the standard in this case was to do a count after a set period of time. In this method general coliform and fecal coliform bacterial colonies show up as diferent colors allowing differentiation. Because determining bacterial concentration requires incubating a sample for 24-48 hrs we will not be doing this for our lab.

Habitat Assessment Data Sheet (Low Gradient- Multiple Habitat Approach)

Details on filling out the Habitat Assessment Data Sheet


Big Creek Reserve Water Quality Data
Date Air Temp Water Temp DO pH Conductivity
  *C *C mg/l mS
7/21/1999 24.5 15 9.6 8.5
8/24/1999 16.3 13.6 8.7 8.4 270
9/20/1999 16.3 14 7.3 8.5 327.5
1/3/2000 12 10.1 11.5 8.9 337.5
1/9/2000 10.4 10.6 11.4 8.7 300
1/19/2000 14 13.8 9.9 9 195
1/25/2000 16.3 12.8 10 7.7 302.6
2/9/2000 13.1 12.4 10.2 8.2 180
2/16/2000 11.2 13 10.6 8.5 279.5
2/19/2000 19 11.3 8.5 292
2/20/2000 8.5 11.6 8.4 236
2/22/2000 13 10.7 8.5 300
2/24/2000 11 12.6 8.5 284
3/1/2000 15 12.4 8.6 320
3/15/2000 16.5 13.6 9.9 8.6 300
4/10/2000 17.1 14.2 10.3 8.6 325
4/17/2000 15.8 12.8 10 8.5 299
5/3/2000 15.7 13.9 8.8 8.6 350
5/15/2000 15.6 14.1 8.6 8.7 347
6/6/2000 17.7 15.7 8.6 8.6 348
6/22/2000 17.3 16.1 7.3 8.6 350
7/27/2000 21.7 17 8.7 8.4 352
9/16/2000 14.7 15.2 8.2 8.2 364
10/14/2000 17.3 13.7 8.2 8.2 372
11/18/2000 11 9.3 9.2 8.1 372
12/2/2000 13.3 10.7 9 8.2 375
12/9/2000 13 12.2 8.5 8.2 367
1/13/2001 12.8 9.5 12.1 8.3 309
5/24/2001 17.7 17.7 8.1 307
6/8/2001 18.3 17.3 9.6 8.3 339
7/15/2001 16.4 16.4 9.6 332
11/23/2001 14.5 13.3 10.9 7.9 363
1/13/2002 11.9 11 13.6 8.1 318
2/9/2002 11.9 9.5 15.7 8.5 273
2/25/2002 8.9 10.1 14.4 8 297
4/7/2002 12.4 10.9 14.2 7.8 277
6/2/2002 13.7 10.9 9.7 8.3 297
6/23/2002 17.1 13.4 9.4 8.2 277
7/20/2002 14 14.3 9.7 8.4 307
9/15/2002 15.5 14.6 9.8 8.4 320
10/23/2002 15.3 14.8 7.9 8.4 290


 Copyright Notice and Credits
Revised 26 January, 2015
Bio 130 Student Information Page Our Raccoon will bring you home Biological Sciences Home Page