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BENTHIC CYANOBACTERIA COVERAGE SOP
P R E P A R E D B Y
U P D A T E D V E R S I O N
A P P R O V A L S
Utah Benthic Cyanobacteria Workgroup
8 October 2024 3.0
_______________________________________
Toby Hooker, PhD, QA Oicer, UDWQ Date
_______________________________________ Ben Brown, Section Manager, UDWQ Date
1. Overview
This document presents the Utah Division of Water Quality’s DWQ Standard Operating Procedure
SOP for monitoring benthic cyanobacteria percent coverage in streams, rivers, and lentic systems
with recreational use.
This protocol is designed to be used in areas where known benthic cyanobacteria (order
Oscillatoriales) are present. Monitoring locations should be identified based on recreational
exposure potential. While pets and animals may also be impacted by benthic cyanobacteria, current
statewide guidance is focused on evaluating risk to human health. This means sites where people
are likely to engage in primary contact recreation such as swimming, bathing, waterplay, and
paddling/floating. This may also include sites where backpackers, hikers, or river rafters filter
drinking water.
This SOP is followed by all DWQ monitors and is recommended as the procedure for DWQ
cooperators or local health department LHD sta performing benthic cyanobacteria monitoring.
1.1 Health and safety warnings
Benthic cyanobacteria mats may contain toxin-producing species. Samplers should always wear
gloves and waders/boots during sampling.
Cyanotoxin exposure is most likely to occur when an individual comes into direct contact with a mat.
Disturbed or naturally detaching mats may release dissolved toxins into the overlying water column.
Ingestion of mat material itself is particularly hazardous. Common symptoms include: diarrhea,
vomiting, numb lips, tingling fingers, dizziness, asthma-like symptoms, and skin irritation. If any of
these symptoms occur, monitors should leave the impacted area and seek medical treatment
immediately. Follow Human Resources procedures on reporting any sickness/injury.
Field personnel should be aware that hazardous conditions potentially exist at every waterbody. If
unfavorable conditions are present at the time of sampling, the sample visit should be rescheduled.
If hazardous weather conditions arise during sampling, such as lightning or high flow, personnel
should cease sampling and move to a safe location.
1.2 Equipment and supplies
Copy of this SOP
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Protective equipment: gloves, chest/hip waders
Phone/tablet with Survey123 data form
50 100 m tape measure
Bathyscope
Quadrat 0.25 x 0.5 m) with a 0.1m grid
Polyethylene bole for taxonomic sampling
Amber glass bole for toxin sampling (optional)
2. Procedure
Key steps in the procedure are:
● Walk the area to be assessed and evaluate whether benthic cyanobacteria are present
● If benthic cyanobacteria are present, collect a percent coverage estimate along five
transects
● Start your first transect in an area of high recreational usage and measure percent coverage
using a point-intercept method
● Estimate cover of benthic cyanobacterial mat along the remaining transects working
upstream
2.1 Visual assessment
Walk the full length of the recreation area. At a minimum this should include a 50 m distance of
stream bank or shoreline. Minimize disturbance of benthic material in the waterbody, walking on
shore as much as possible. While walking the area, qualitatively evaluate the site for benthic
cyanobacteria (order Oscillatoriales). Also take note of water turbidity and any evidence of flooding.
→ If no benthic cyanobacteria is present, no further monitoring is required during this visit.
Note: If you see benthic growth but are uncertain about whether it is or is not benthic cyanobacteria, collect
a taxonomic sample or samples of material in question and take photos (see Section 3.1). Proceed with the
assumption that what you are seeing is benthic cyanobacteria, but make a note of the samples collected and
growth types you are uncertain about in the notes section of the field form so that your results can be
reinterpreted if necessary following taxonomic analysis.
→ If benthic cyanobacteria is present, determine if the mats pose high recreational risk. This
includes detached mats accumulating on the shoreline; enclosed lentic systems; and sites where
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recreational contact with mats is likely. See Table 1. If mats pose high risk make sure to take photos
carefully documenting the qualifiers detailed in Table 1 and record observations in the survey.
Table 1. Qualifiers for high recreational risk and descriptions.
High risk qualifier Description
Cyanobacteria mats accumulating on the shore Mats that have become detached are accumulating along the shoreline or on the shore. This includes
both wet and dried mats
Floating cyanobacteria mats Floating mats are observed in stagnant areas or
floating downstream while surveying
Enclosed lentic systems The waterbody being assessed is a small pond or other enclosed lentic system. Any
disturbed/detached mats are likely to come in contact with potential recreators
Recreational contact with mats likely Mat placement and/or size such that mats are likely
to come into contact with potential recreators
2.2 Establish your first transect
Identify an area of high recreation to start your sampling reach. This often will be the main area
where recreators are entering the water. Your first transect will be in this area. Four additional
transects will be established upstream at 10 m intervals.
Transects will run across the water in locations where the depth is <2 ft. If the water is deeper, run
your transect from shore and stop when the water is >2 ft.
Set your first transect by spreading a measuring tape between the shore and the transect end
point. As you set your transect, be sure to walk on the downstream side of the tape measure to
avoid disturbance.
If the wadeable width of the waterbody is too narrow to allow for five quadrats to be placed easily
side-by-side (i.e., generally <5 m), the transect may instead be zigzagged in five lengths of 10 m.
See Figure 1 for illustration of quadrat layouts in both flowing and standing waters.
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Figure 1. Transect (T1-T5 layouts for flowing and standing waterbodies of varying widths and depths.
Record weed width. Divide the measured distance into five roughly equal increments. Using a
quadrat with a ten-measurement grid spaced 0.1 m apart, take measurements at each of the five
increments, aligning the quadrat perpendicular to flow. For segments along the bank, place the
quadrat in the water directly along the shore. See Figure 2.
→ Once your first transect is established, you will collect coverage measurements.
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Figure 2. Overhead figure of five transects with five quadrat readings per transect in a river system.
2.3 Collect coverage measurements
Stand on the downstream side of the tape and set the quadrat at your first designated point on the
upstream side of your measuring tape. At each of the ten points on the quadrat, look directly down.
Use a bathyscope to view each cross point. Indicate whether benthic cyanobacteria is present or
absent directly below each of the 10 points. Count the number of hits and the number of misses and
record these in the survey (see Figure 3).
Note: If the water is turbid or hard to see through, you may use a gloved hand to pull up a rock or small piece of
mat material to check for presence/absence. This field method may not work in highly turbid waters.
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Figure 3. Looking down at a quadrat. “Present” is indicated whenever an intersection is directly above a
benthic cyanobacteria mat.
Move the quadrat to the additional four locations along the transect and repeat observations of
presence/absence. At the end of the transect, you will have a total of fifty points.
→ Once you finish the transect, record general observations of benthic mats, substrate, and flow.
These observations are summarized in Table 2.
Table 2. Additional observations collected for each transect.
Variable Options
Relative size of the largest benthic mat intercepted
across the transect
● Smaller than a quarter
● Quarter to deck of cards
● Deck of cards to leer sized paper
● Leer sized paper to a doormat
● Larger than a doormat
Most common substrate size along the transect ● Clay - slick and hard clay (not griy)
● Sand - smaller than a ladybug
● Fine gravel - ladybug to marble
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● Coarse gravel - marble to tennis ball
● Cobble - tennis ball to basketball
● Boulder - basketball to car
● Bedrock - bigger than a car
Most common stream bed feature along your
transect (flowing waterbodies only)
● Rie - fastest; shallow flow with turbulent
water
● Pool - slowest; slow flow with calm water
● Run - between a pool and rie; deep and
fast flowing water, with lile or no turbulence
You will also record approximate weed width of the transect and distance between transects
(typically 10 m unless additional spacing required to avoid an obstacle).
2.4 Collect additional transect data
→ Once you are fully finished with your first transect, use a tape measure to set your next
transect 10 m upstream from your first transect. Be careful not to “cut corners” or bends in the
stream.
Check the conditions of the site while seing the transects to observe any safety concerns that
might require the site to be moved (e.g., deep holes, rebar, loose rocks, etc.). If necessary, move your
transect 5 meters upstream.
Set up your second transect and repeat the measurements collected for the first transect and
record observations.
Repeat this process until you have completed five transects along your reach, for a total of 250
present/absent points.
→ Divide your “present” measurements by 250 to calculate percent cover for the entire reach.
3. Sample collection (as needed)
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Phycology samples may be collected when a monitor is uncertain about whether observed benthic
growth is cyanobacteria. Toxin samples may be collected upon request to expand monitoring data.
Coordinate any sample collection with DWQ.
3.1 Collecting a phycology sample
To collect a phycology sample:
● Make sure you have taken photos of the material to be sampled as part of your visual survey
● Use a polyethylene bole (usually 250 mL)
● With gloved hands, fill the bole with mat material. Try to put only one “type” of mat material
in each sample bole
● Add site water to the bole until the mat material is submerged
● Label the bole with the location, date, and time of sample
● Immediately store the sample on ice or in the refrigerator. For accurate results, the sample
needs to be delivered within 48 hrs (on ice) to the analyzing lab. Usually this requires
overnight shipping on ice. Delivery time can be extended if a preservative (usually
glutaraldehyde) is added. Preference is for live samples. Consult with UDWQ or PhycoTech for
preservative usage.
Samples are analyzed by PhycoTech, Inc. Coordinate directly with UDWQ for sample submission.
3.2 Collecting a toxin sample
In the event a toxin sample is requested:
● Take photos of the material to be sampled as part of your visual survey
● Use an amber glass bole (usually 100 250 mL). This will be provided by the analyzing lab
and, depending on the toxin being analyzed for, may contain preservative
● With gloved hands, fill the bole with mat material. Material from multiple mats 8 10 if
possible) is ideal and the size of pieces from mats should be roughly equivalent. Toxin
production is very heterogeneous, so you want to sample from multiple areas of growth
on-site. If present, be careful not to spill any preservative
● Label the bole with the location, date, and time of sample. Note the wet volume of the
collected material
● Immediately store the sample on ice or in the refrigerator. For accurate results, the sample
needs to be delivered within 48 hrs (on ice) to the analyzing lab. Usually this requires
overnight shipping on ice. Alternatively, samples can be immediately frozen and stored in a
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freezer for up to 1 month before shipment. Shipment of frozen samples should still be
overnight and on ice
Toxin samples are usually analyzed by the UDAF or Regional EPA lab. Coordinate directly with UDWQ
for sample submission.
Data and quality management
All data recorded in the field should be reviewed for completeness before leaving the sample site.
Data is returned to DWQ to be reviewed by the project manager, stored and shared with LHD’s and
stakeholders for advisory decisions. All field data will be managed and stored using current
DWQ Monitoring Section data management guidelines.
One intercept coverage measurement will be repeated at each site by a second monitor. These
observations will be used to run inter-analyst comparisons for quality assurance. Any other QA/QC
procedures should be addressed on a project-by-project basis in the SAP for the project.
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