FISH: First Investigation of Stream Health

Instructions

This project is a community science monitoring protocol for detecting early signs of stream improvements in the watershed. Monitoring your stream will help show the positive impacts of stream restoration activities on stream health. See additional resources or

Introduction

This First Investigation of Stream Health (FISH) protocol will take you step by step through a series of tasks to observe water quality indicators, macroinvertebrates, wildlife, vegetation cover and quality, stream bottom habitat, water clarity, and more. It can be used to better understand the health of a stream at the time it is being observed. It can also be used to track changes over time and is helpful for observing how a stream can improve within a few growing seasons after a restoration project has begun. A restoration project could include planting streamside trees or shrubs, stabilizing a streambank, live staking, or fencing out livestock and domestic animals. To track changes over time, choose a stream to monitor that you have permission to access and is safe to access. It is best if you can complete the FISH protocol during the spring and fall seasons for at least 3 years.

Through time, the vegetation structure of your stream will change and grow. As it matures, the habitat will become more complex, and you will likely see an increase in the number and variety of plant and animal species. Enjoy the progress as you witness the changes!

Getting Started

Identify landmarks along your stream, marking the start and end of the section of stream you plan to monitor. Landmarks could be property boundaries or large trees, rocks, fence rows, bends in the stream, or other landscape features. Ideally, the section should be between 100 and 300 feet long.

The following sections describe specific aspects of the stream that you should monitor and that correspond to the FISH data collection sheet. We encourage you to collect as much information as possible each time you monitor your stream and at least once each year.

Water Clarity

Transparency

Transparency is a measure of the particles suspended in the water including soil and algae. It is a measure of water clarity and an indicator of water quality. Having clear water can be a sign of clean water and is an important habitat characteristic for fish and other stream organisms. Use a transparency tube to measure the first depth at which you can still see the symbol at the bottom of your tube, and record the measurement in centimeters. This is an optional data field in the protocol.

For more information, visit Understanding Transparency Tube Measurements.

Stream Bottom Habitats

Embeddedness

Embeddedness is the extent to which the rocks and gravel of a stream bottom are covered in fine silt or sediment. The healthiest habitats for macroinvertebrates, or aquatic bugs, are the small spaces within a stream, which are created by rocks and gravel. However, fine sediment can fill up those holes, making it hard for insects to survive.

Rate your section of stream on how embedded the gravel and rocks are in fine sediment from 1–9, with 1 being highly embedded and 9 being very low in embeddedness.

• High embeddedness is indicated if the stream bottom is entirely mud and no rocks or gravel are visible. Embeddedness is also high if rocks are present but they are packed down into mud and hard to remove from the stream bottom.
• Medium embeddedness is indicated if the stream bottom is a mix of rocks and mud. Embeddedness is also medium if the stones are easily removed but mud is still visible underneath.
• Low embeddedness is indicated if the stream bottom is entirely rocky and little to no sediment or mud is visible.

If you need another way to determine embeddedness, you can wade into the stream. As you walk, notice if a large sediment cloud forms with each step or if the water stays clear with no mud disturbed. A stream with a higher level of embeddedness will create a larger mud cloud when the bottom is disturbed. Your feet might even sink into the sediment. Embeddedness can often vary within a stream section. Do your best to record an average score for the entire section of stream being studied.

Stream Life

Note: Please be very careful to replace rocks, logs, and branches as you found them to maintain habitat integrity for riparian (streamside) insects and salamanders!

Macroinvertebrates

Macroinvertebrates, or aquatic bugs, form the base of the food web for aquatic life. Pick two locations within the stream and flip over five rocks at each location. Search for bugs crawling over the bottom or sides of the rocks. Count and record how many of these aquatic bugs you see. Return the rocks to their original position when recording is complete. Try to revisit the same two locations each time you complete FISH.

Also try to identify the different bugs you found. Several phone apps are available to help with macroinvertebrate identification. Taking a photo can help you identify the macroinvertebrate later when you have access to the internet or identification guides. If you can identify the bugs, you can record whether the ones you found are good, medium, or poor indicators of stream health. However, if you cannot spend time on identification, make a note of how many kinds of aquatic bugs you found. Different macroinvertebrates will be present during different times of the year. Due to these natural fluxes in populations throughout the year, only compare your macroinvertebrate observations taken at a similar time of year.

Note: If you collect or move the bugs, you need a fishing license.

Amphibians (salamanders and frogs)

Amphibians can live either on land (terrestrial) or in water (aquatic). These animals primarily breathe through their skin and are sensitive to chemical pollutants, toxins, and sediments suspended in the water. They also require moist, shady environments and places to hide such as under logs or rocks to help them maintain their moist skin to breathe and regulate their body temperature. Because of these characteristics, they are excellent indicators of environmental health.

The variety and number of salamanders and frogs will likely increase as your riparian buffer matures. The riparian buffer is the area alongside a river or other body of water including natural vegetation such as trees, shrubs, or tall (non-turf) grasses. Pick three locations along the stream and flip rocks/logs in an area of 6 feet by 6 feet at each location. Try to include a variety of areas, such as in the water, on the water’s edge, and within the buffer close to the stream. Provide a total count of amphibians seen when you flip over rocks and logs in and along the edge of the stream. It is important to return the rocks and logs to their original position when you complete the observations. Try to identify the salamanders and frogs you find. Like with the macroinvertebrates, you need a fishing license if you collect or move the amphibians.

Tip: Flip rocks toward you and look over them to create a barrier between you and any critters that might be underneath.

Fish

The presence and type of riparian buffer vegetation can have a significant impact on the presence of fish in the stream. Coldwater fishes require trees within the buffer that can help provide canopy shade over the stream. Spend 1–2 minutes observing your stretch of stream. Record how many kinds of fish and the total of each type you observe. If you can, include the identifications of the fish you see.

Birds

The identification of birds is a life-long quest in learning, but you do not have to be an expert to enjoy our feathered friends. Different birds will favor different habitats, including ground and shrubs, dense vegetation, open vegetation, fields, or tree canopies. Note the various sizes and shapes of birds you observe in the different riparian buffer habitats, which will help you understand how your riparian buffer is being used. If possible, group the number of birds you see in these common categories: woodpeckers (e.g. red-bellied woodpecker), waterfowl (e.g. mallards), raptors (hawks or owls), small birds (sparrows), or unknown. A larger diversity of birds can indicate that a healthy plant and insect community is supporting those birds and their young. You may not always see the birds but instead you may hear them. Note those birds as well

Scat, Tracks, and Signs

Wildlife Signs

Wildlife often goes unnoticed, but they frequently leave behind evidence that they were there. We must look closely and learn to recognize those signs. You may see scat (the scientific term for animal poop), tracks (also known as footprints), or other signs such as broken branches, nibbled seedlings, nests, slides in the mud, or runways in the grass. Take note of any scat, tracks, and other signs you see and record them.

General Wildlife Observations

Record any other wildlife species that have not yet been recorded while you were out experiencing your section of the creek. Note any details (e.g., shape, size, color, bill length, wing shape, and antlers) that will help you record species identifications later. You can also make notes about any wildlife activity you witnessed.

Vegetation

Bank Cover

Fast-moving water can erode the banks on either side of a stream. Erosion causes loose soil, called sediment, to break free and be transported downstream by the water. Sediment can cover important stream habitats, alter stream flow, and increase nutrients to harmful levels. Established vegetation on the banks can help prevent erosion. Use a scale from 1 to 9 to rate how much each streambank is covered in vegetation. Estimate an average value of the entire length for each side of the stream.

• A score of 1 would be poorly vegetated with no vegetation on the bank. Banks may be steep with evidence of severe erosion.
• A middle score would be partially vegetated with areas where plants have established but other areas have bare soil. Some erosion might be evident.
• A score of 9 would be fully vegetated with little or no bare spots and little sign of erosion.

Note: This score does not consider the quality of vegetation present, only the amount of stream bank cover.

Riparian Zone

The area surrounding a stream is known as the riparian zone. If there is permanent vegetation growing in that riparian zone, it is called a riparian buffer. It is very important for trees, shrubs, and other vegetation to exist along and extend out from a stream. Measure the riparian buffer from the stream edge until human disturbance (mowed lawn, pasture, row crop, road, etc.). The wider the area and the more mature the vegetation, the more benefits the riparian buffer provides. Trees shade the stream, reducing water temperature and creating a more suitable habitat for fish. Vegetation holds the soil in place, absorbs pollutants, and provides homes for birds, small mammals, and other wildlife. Trees provide more stream-health benefits than shrubs, and shrubs provide more benefits than grass. Rate the quality of the riparian vegetation using a 1 to 9 scale.

• A score of 1 would be mostly grass within the riparian zone.
• A middle score would include a mix of grasses, shrubs, and some trees.
• A riparian zone with an abundance of mature trees would be a score of 9.

Vegetative cover As mentioned above, vegetation along the banks and within the riparian zone is crucial for healthy watersheds because it helps prevent soil loss through erosion and can absorb pollutants before they reach the stream. Regardless of the plant type, the roots of the plant help hold onto the soil and prevent it from running off into the stream, causing sediment pollution. Vegetative cover can also be leaf litter, which not only creates a microhabitat for many organisms but also can help slow down erosion. Assess the riparian zone and record an average percentage of vegetative cover for your stream site. Note: This score does not consider the quality of vegetation present, only the amount of riparian zone covered by vegetation.

Native plants

Native plants are those that have been known to grow naturally in an area since before colonialization. Non-native, and sometimes invasive, species have been introduced from other regions or countries. Insects and wildlife prefer, and oftentimes require, native plant species for food and nesting. For this reason, non-native and invasive species can be detrimental to wildlife habitats. Some common non-native species in Pennsylvania include multiflora rose, oriental bittersweet, burning bush, invasive honeysuckle, invasive hops, bamboo, mile-a-minute, and invasive stilt grass. If you can identify the plants growing at your site and determine if they are native or non-native, note what percentage of the vegetation is native. Plant identification guides will often indicate a plant's location of origin.

Snags

Standing dead trees, also called snags, provide nesting and roosting habitats for many types of wildlife including songbirds, bats, small mammals, woodpeckers, raccoons, flying squirrels, and many more. The size of the tree is important because the bigger the tree, the longer it will last, and the larger the type of wildlife that can use it. Estimate the width across the trunk of the tree in inches, at about 4 feet off the ground.

Large woody debris

Fallen trees, logs, and branches within the stream and at least 4 inches wide and 6 feet long are called large woody debris. Large woody debris has many benefits to stream health. It provides an obstacle during times of high water flow and decreases the velocity of water, which helps to reduce soil erosion and sedimentation, while also diverting some water into the floodplain. Large woody debris also adds crucial aquatic habitat to the stream. Logs are used by basking turtles and snakes or as a perch for waterfowl hunting fish. Underwater, the large woody debris provides habitat and shelter for fish and other organisms. Estimate whether the woody debris observed is more or less than your last visit. You can learn more about the benefits of large woody debris in streams in the following extension article "Benefits of Large Woody Debris in Streams".

Other Notes

If there are any other observations or notes about your site, be sure to include them. If you participate in other monitoring programs, feel free to record those results here as well for easy comparisons.

Additional Resources

For other FISH-related information (species identification resources, answers to common questions, webinars, and more), please visit extension.psu.edu/FISH. You can learn about other monitoring opportunities in Pennsylvania by reaching out to the extension Master Watershed Stewards. If you live outside Pennsylvania, contact your local extension office.