Adapt your field sampling to each reach (but stay comparable)

All flowing sites (upstream/midstream):

• Cross-section composites: At a fixed transect, collect a discharge-weighted composite using EWI (Equal-Width Increment; 10–20 verticals) or EDI (Equal-Discharge Increment; ~4–9 verticals). Use an isokinetic depth-integrating sampler (or a pump at constant rate) and integrate from surface to near-bed without touching the bottom. This avoids over-representing slow banks/eddies or fast thalweg water. U.S. Geological Surveynemi.govUSGS
• Shallow & rocky/fast: Wading is OK but keep the nozzle centered in flow, move smoothly to avoid turbulence and bed scour. If depth/velocity are too high for depth-integrating gear, take multiple point samples in proportion to local discharge and combine to a composite. U.S. Geological Survey

Deep, slow, or tidally influenced (downstream/near sea):

• Vertical structure matters: Use a Van Dorn/Niskin or pump to collect discrete depths (surface, mid, ~1–2 m above bed) or a depth-integrated tube if stratification is weak; then combine into a whole-water composite for phytoplankton counts.
• Tide timing: Sample at a consistent tidal stage (e.g., mid-ebb each month) to reduce estuarine mixing effects; record stage and salinity profile. (Standard hydrology/estuary QA practice; align with your program SOP.)

Light/“photic zone” targeting (optional but better):

• If you have a PAR meter, integrate the upper layer down to the 1% surface light depth; if not, record Secchi depth and keep that metadata—useful for later normalizations and chlorophyll stratification decisions referenced in UNESCO guidance. UNESCO Documents

2) Make sure samples actually contain phytoplankton

For quantitative abundance & community composition (what you usually need for ecology/water-quality):

• Always take whole-water (“bulk”) samples, not just net tows. Nets miss small cells (picoplankton & nanoplankton) and give biased counts. Preserve whole-water immediately. repository.oceanbestpractices.orgIteh Standards
• Preservation: Add acidic Lugol’s iodine to ~1% final volume (brown-tea color), invert gently, keep cool and dark until analysis. This is the standard for Utermöhl counting. US EPAfiles.nc.gov
• Microscopy method: In the lab, settle known volumes in chambers and count with inverted microscopy (Utermöhl technique) following EN 15204:2006 / IOC-UNESCO guides. Report as cells L⁻¹ (and biovolume if you estimate cell dimensions). repository.oceanbestpractices.orgiTeh Standardscdn.ioos.noaa.gov

For supporting indicators / verification:

• Chlorophyll-a: Filter a known volume onto GF/F (or 0.7 µm equivalent), extract in 90% acetone (dark, cold), read fluorometrically (e.g., EPA Method 445.0 / SM 10200H). This corroborates that phytoplankton biomass was present even if cell counts are low. nemi.govEPA NERLumces.edu
• Optional net tow (qualitative): A 20 μm plankton net tow at each site helps detect rare/large taxa, but label these “qualitative presence/absence,” not for density. (USGS parameter codes include PHYTOPLANKTON-NET as a distinct method.) USGS

3) Site-specific tweaks you can apply immediately

• Fast, rocky reaches: Expect low suspended biomass and more periphyton on stones. If phytoplankton densities are near detection limits, increase bulk sample volume (e.g., 2–5 L) so you can settle larger volumes (e.g., 50–100 mL) in Utermöhl chambers. Consider adding a standardized periphyton scrape (area-based) as a companion metric to explain low plankton counts. (Periphyton SOPs are common in EPA/US state programs aligned with phytoplankton SOPs.) files.nc.gov
• Deep/slow/turbid reaches: Expect higher suspended biomass; avoid near-bed resuspension. If salinity intrudes, treat salinity strata as separate “micro-habitats” or composite within strata to keep comparability.

4) Replication, QC, and metadata (keeps your stats honest)

• Replicates: At least field duplicates at 10% of stations; split lab replicates for counts and chlorophyll.
• Blanks: Equipment/field blanks when using pumps/tubing to check contamination/preservatives.
• Core metadata: GPS, date/time, flow/tide stage, temperature, conductivity/salinity, turbidity/Secchi, nutrients (TP, TN, nitrate, SRP), and notes on recent rain—key covariates for interpreting phytoplankton.
• Counting QA: Follow EN 15204 counting rules (minimum cell counts/fields, precision checks) and IOC-UNESCO guidance for taxonomic consistency. repository.oceanbestpractices.orgcdn.ioos.noaa.gov

5) Minimal gear list that works in all three zones

• Depth-integrating sampler or constant-rate pump with intake rod; Van Dorn/Niskin for discrete depths; plankton net (20 μm) for qualitative tows; dark bottles; Lugol’s iodine; GF/F filters + filtration rig; cool box; Secchi disk; optional PAR meter.

6) Short reading list / SOPs you can lean on

• Cross-section compositing in rivers: USGS EWI/EDI guidance and overview. U.S. Geological Surveynemi.govUSGS
• Phytoplankton counting standard: EN 15204:2006 (Utermöhl). repository.oceanbestpractices.orgiTeh Standards
• IOC-UNESCO Manual: Microscopic and Molecular Methods for Quantitative Phytoplankton Analysis (2010). Clear chapters on Utermöhl and alternatives. UNESCO Documentscdn.ioos.noaa.gov
• EPA/State SOP example: Phytoplankton analysis (Modified Utermöhl) & preservation details (Lugol’s). US EPAfiles.nc.gov
• Chlorophyll-a method: EPA 445.0 and aligned university SOPs. nemi.govEPA NERLumces.edu

The Utermöhl technique can be equipment-intensive. Not everyone has access to an inverted microscope and counting chambers. An alternative could be to use a membrane filter. After the filter has air-dried, it can be made transparent with immersion oil. I have not seen this method compared to the Utermöhl technique. Attached is a picture of plankton on a membrane filter. On the right side I have used red spots to mark the algae as I counted.