First Investigation of Stream Health (FISH) Protocol

Do you enjoy outdoor activities? Become a citizen scientist. First Investigation of Stream Health (FISH) monitors changes to local streams and their habitats.
First Investigation of Stream Health (FISH) Protocol - Articles

Updated: August 8, 2017

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First Investigation of Stream Health (FISH) Protocol

FISH is a simple, family-friendly activity that asks easy to answer questions about what you see around a stream. Recording with FISH helps you and others understand how the health of the stream habitat is changing over time.

You can participate in FISH using the paper FISH survey, the FISH website entry form, and using FISH mobile apps.

FISH is designed to be taken out to a stream restoration site (riparian buffer planting, stream bank fencing installation, live staking, etc.) There you will make observations about various stream health indicators like water clarity, growth of vegetation, and signs of wildlife.

The FISH Protocol survey should be completed at least once a year in the spring, but additional observations made in the summer and fall might also be valuable to you. Trained FISH participants are asked to complete the survey for at least three years, but are encouraged to monitor for up to ten years or more.

If you use the paper survey, we encourage you to enter the results from your surveys online. You can also maintain your own hard copies so that you can see first hand the successes of your efforts.

The original FISH Protocol was developed by Penn State Extension and the Penn State Agriculture & Environment Center as a project of the Conewago Creek Initiative. The website and mobile apps were developed by Chesapeake Commons as part of the Greening the Lower Susquehanna project. Both projects were funded by the National Fish and Wildlife Foundation (NFWF).

Additional Resources to help you with FISH

When making observations, it may be helpful to refer to some additional resources as a guide to identifying what you see. Here are some resources you might consider:

Identifying Stream Bugs (Macroinvertebrates)

Identifying Fish, Reptiles, and Amphibians

Interpreting Results

  • See... Understanding Your Transparency Tube Measurements

The timing of these events can be influenced by a combination of factors including rainfall, soil, water and air temperature, moisture levels and photoperiod. In central Pennsylvania there are three distinct periods in which potential species can be expected to begin breeding. These periods, and the species that breed in them are as follows:

Early Spring (March 15 - April 15)

In most years this period typically begins in mid-March and lasts until mid-April. Depending on the temperatures and precipitation patterns over the winter some species can emerge as early as mid- February and begin calling in early March. Species that chorus during this period include:

  • spring peeper (usually the first to begin chorus - peaks in April)
  • northern leopard frog
  • wood frog (very short chorus period - sometimes only a week)
  • American toad

Spring (April 15 - May 15)

  • mountain chorus frog (requires air temp >41° F)
  • green frog
  • pickerel frog

Summer (May 15 - August)

In most years this period typically begins in mid-May and lasts through the summer months. Species that chorus during this period include:

  • Fowler's toad
  • gray treefrog (peaks in June)
  • bullfrog


Transparency tubes can be made or purchased.

What is a Transparency Tube?

A transparency tube is a relatively new piece of equipment that has become popular for use in volunteer stream monitoring programs and for educational activities. They came into use in the mid-90's as a way to apply the principles of measuring water clarity using a secchi disk to shallow bodies of water where a secchi disk in unusable. Secchi disks have been used since the 1800's. They are round disks, usually about 8-10 inches in diameter, with a high-contrast black and white pattern printed on them. Typically that pattern is in wedges, like shown in the illustration. Secchi disks are lowered into lakes and ponds, tied to a rope, until the point where they are just barely visible. The distance along the rope is then measured to the water's surface, and a that length is recorded as the water's transparency measurement.

Applying a secchi disk to a shallow stream, or even a deep stream, is often not realistic. Either the water is not deep enough for the disk to become not visible, or the current carries the disc downstream and prevents a reading. The transparency tube, as shown in the illustration above, is a clear (typically plastic) tube that can be filled with water from a stream (or any body of water) to create a vertical column of water. The user then looks down though the water to identify the depth at which a smaller secchi disk, printed in the bottom of the tube, can be seen. Some transparency tubes have drain hoses at the bottom to lower the water column; others need to be carefully poured out in small amounts.

What do the Results Mean?

A secchi disk measures water clarity in terms of transparency (the ability for light to penetrate the water.) The transparency of water is important for a number of reasons. Plants growing in the water need sunlight in order to complete photosynthesis. Photosynthesis is how plants make their own food and it also has the fortunate byproduct of producing oxygen which is released into the water, a key to increasing dissolved oxygen levels for aquatic animals to use for respiration. The water's transparency is also important to aquatic animals for navigation, finding food, and avoiding predators. In addition, decreased water transparency is an indicator of other issues that may be occurring, such as high sediment pollution and increased algae growth.

A more scientific measure of water clarity is to measure turbidity using a turbidity meter or test kit. Turbidity is measured by determining the height of a column of water that is needed to completely obscure a beam of light. Technological advancements over time have changed exactly how this measurement is accomplished, and in what units turbidity measurements are recorded. For the most part, modern measurements are made using a meter referred to as a nephelometer, and results are recorded in units called Nephelometric Turbidity Units (NTU).

When discussing the effects of varying levels of water clarity on the environment, wildlife, and even humans, you will usually see clarity referred to in turbidity units (such as NTU, or somewhat equivalent FTU or JTU measurements.) Transparency measurements recorded using a transparency tube can be converted to NTU values using the conversion chart given here.

cmNTUcmNTUcmNTU
<6.4>24021.7 to 24.13544.6 to 47.013
6.4 to 7.024024.2 to 26.73047.1 to 49.512
7.1 to 8.218528.8 to 29.22749.6 to 52.111
8.3 to 9.515029.3 to 31.82452.2 to 54.610
9.6 to 10.812031.9 to 34.32154.7 to 579
10.9 to 12.010034.4 to 36.81957 to 608
12.1 to 14.09036.9 to 39.41760 to 707
14.1 to 16.56539.5 ti 41.91570 to 856
16.6 to 19.14042.0 to 44.514>85<5
19.2 to 21.640

A few key measurements to consider as benchmarks for water clarity include:

  • >10 NTU = Fish and other aquatic wildlife begin to demonstrate signs of stress.
  • 1-5 NTU = EPA Drinking Water Standards (depending on the type of filtration system in place)
  • >5 NTU = not recommended for recreational use

Tips for Using a Transparency Tube

  • Follow the instructions that accompany your purchased transparency tube or the plans you used for making your own tube.
  • If you wade into the stream to collect water, collect upstream from where you have walked to avoid collecting sediment disturbed by your feet.
  • Don't let the tip of the transparency tube touch the stream bottom and disturb sediment while filling.
  • Attempt to take your measurements in indirect sunlight to keep comparisons as consistent as possible.
  • Record current weather conditions, including cloud cover, and any significant weather that occurred in the days prior to your measurement. Also record the time of day. This information will help you identify why you might be seeing big differences between measurements.

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