The initial stage of a stream study is the same as for any other science. First, the biologist, on the basis of what she knows about the stream, sees an unsolved problem, and comes up with a hypothesis: a possible reason for why something is the way it is. (For example, the problem may be why some organisms aren't doing well in the stream. The biologist's hypothesis may be that the stream is polluted).
To be able to think of a good hypothesis, she will spend time in a library, read journals, and talk to biologists to find out what is already known. She might even talk to members of the community. Then she must decide what kinds of data (factual information) she could collect that might help her disprove her hypothesis. It's important to realize that scientists don't try to prove hypotheses, they try to disprove them. There is no way to prove anything. All we can hope to do is disprove ideas, and even that is open to argument.
Data is collected in samples. A sample could be macroinvertebrates, fish, algae, collections of organic material, water, sediment. Samples are often simply lists of numbers: various readings and measurements of organisms, water, and so on. Samples can even be photographs and drawings. The biologist must figure out what method to use in order to collect her samples. He will also figure out how many samples to collect, what size the samples should be, where they should be collected, and the frequency of collection (if he should just collect them once or if he needs to collect samples using the same method several times, or even over a whole year or more). Collection of samples (field work) is a pretty small part of a biologist's year, since he will need plenty of time to work up the samples to find out what they have to tell him. Field work is also time consuming and very expensive. That's why people who volunteer to do collection can be such a big help to biologists.
To collect samples of the stream's organisms, many methods are used, depending on what the biologist is after. To collect fish data, she may just elect to observe them in their natural setting. To do this, she puts on diving gear and a snorkel and watches them underwater, writing on a waterproof piece of plastic.
She may need to see the fish close up, though, and for this, nets, electroshock, or fly-fishing may be used. Nets will usually kill the fish; if she needs to kill them anyway, for stomach samples or other laboratory work, this will be okay. Fly-fishing is a way to catch fish that allows the scientist to return them to the river with a minimum of harm, but it isn't as fast as a net. A common way to collect fish is by using electroshock. In this technique, several people move side-by-side up the stream. The one in the middle, the "shocker," carries a heavy backpack with a battery in it. The equipment is set to deliver just enough shock and no more. The shocker uses a long stick with an electrode on the end of it to sweep the water before her, being very careful not to come too close to fish or leave them in the electrical field too long. If a mistake is made in settings or technique, the fish's vertebrae can be fractured. The electricity flowing from the stick stuns fish just enough to make them drift in the current, and the people with nets on either side of her scoop them up and put them in a bucket of water.
Back on shore, the fish are measured. To keep them relaxed (and thus healthier and more able to survive the shock), they are given a little bit of anesthetic in their water. Now their lengths and weights can be taken. A scale might be removed, their fins might be marked so they can be identified later, or their stomach contents might be washed out for later sorting and counting, to see what they have been eating. All of the handling of fishes should be done while wearing cotton gloves to minimize damage to the fish's skin and tissues. Exposure to air should be minimal, fishes should be kept wet at all times, and they should be returned to their spot in the stream as quickly as possible.
If the biologist wishes to collect the tiny organisms on the the stream's bottom (benthic macroinvertebrates), he will often use a Surber sampler. This is a device that allows him to cover a prescribed area of the bottom, pick up the substrate (like rocks) and clean it off, and collect what comes off the substrate into a net. This is a good way to get samples of aquatic invertebrates, like insect larvae, worms, snails, and clams.
Often he will want to sample drift, the matter that is floating along down the stream. Drift is important because it is the main source of food for many fish, including trout and salmon. It may include mayfly larvae that are traveling downstream, dead or dying insects and other small creatures, and terrestrial insects that fall from branches and leaves. To collect this, he uses a drift net with a small mesh, staking it into a spot on the stream and letting the stream flow into it over a certain amount of time. Kick nets can be used to sample small areas quickly. These are most often used by volunteer stream monitors. They are inexpensive (in fact, you can build one yourself) and easy to use. Traps and other more complex methods may even be used.
Specimens should be preserved immediately, since they can deteriorate so quickly. Fishes should be put on ice until they arrive at the lab. Macroinvertebrates should be placed in 70% or 80% ethyl alcohol (a.k.a. ethanol or ETOH). It's safe, inexpensive, and environmentally friendly. Formalin and formaldehyde are carcinogenic chemicals that remain in the environment. Acetone is not a safe chemical to use, either.
Collecting animals isn't the only thing a biologist must do when she visits the stream. At the same time, she will make many other measurements. A lot of stream biology depends on the stream's physical factors: how it's shaped, what's in it, how fast it moves, its temperature, and so on. Knowing all these factors will also help him describe her stream to other scientists who will read her paper to learn from it.
Measuring width and depth are always done, since they are so important. All scientific measurements are done using the metric system (meters, centimeters, and millimeters, instead of yards, feet, and inches). A centimeter is a little less than half an inch.
He will also measure current--how fast the water is moving--in centimeters per second. Although there are traditional ways to do this that you can even do yourself with minimal equipment (an orange peel or leaf, a measuring tape, and a stop-watch), velocimeters are often used today to measure current. Current should be measured at several levels--at the bottom, in the middle, and at the surface--because current often varies throughout that area (called the water column). He will also take the stream's temperature, in degrees Celsius.
Other data that may have value to the biologist's study are the amount of large, woody debris (LWD) lying in the stream, and the amount of tree cover over the stream.
Another important thing to measure is substrate, the bottom of the river. It's important to know just what size the particles are that make up the substrate. A silty, muddy stream is much different from a gravelly stream, and the gravelly stream will be quite different from a stream with large rocks in it.
Sometimes, although not always, she will need to sample the river's chemistry. A lot of this work involves using streamside chemistry kits, and may include pH (how acidic the river is), nitrogen (N), phosphorous (P), and often other chemicals as well, depending on what she is looking for. Dissolved oxygen (DO) is the amount of oxygen that is in the water, and available for animals with gills to use. DO is usually quite high in streams, but in some cases it can be low, and might need to be measured. The biologist can use her streamside chemistry kit to do this, which is a fairly long process, or she can use a computerized instrument with electrodes to do it within seconds.
Stream biologists often measure conductivity with a special handheld meter. If the conductivity is higher or lower than usual at a particular site, they might suspect the presence of pollution--such as sewage leaks, cattle waste, fertilizer, or an oil spill.
Once the samples are preserved, it is time to identify and sort them. This can be an enormous task. If the biologist has collected aquatic invertebrates, he will have to identify and count each one, and there can be hundreds of them in each sample.
To identify an organism, he finds its taxa. Depending on the nature of his study, he will only go so far in identifying each organism. For an environmental study gauging the health of a stream, he might only identify organisms down to class or order, but usually all the way down to family. For more detailed studies, he will use genus. And for very specialized studies, he will attempt to determine the species.
Macroinvertebrates may be colored with a dye like rose bengal to allow the biologist to find them easier amid all the leaves, algae, and other debris. Microscopes are used to assist in identification of tiny bugs, and counts are taken. Samples may be dried out in an oven, then weighed (in grams). Fish stomachs might be removed and preserved separately to look at stomach contents. It is surprising how much a biologist can learn about a fish's last meal. Scales may be flattened and examined under a microscope: scales have rings, and can be read almost like trees' rings.
Finally, when the biologist has finished sorting, counting, and measuring, she will have her data, and it is time to analyze it. She will enter the numbers and other information she has collected into a computer spreadsheet and use her statistics training to analyze the numbers, to see what they might mean. There are standard statistical formulae that will give her the answers she needs. She might use a computer spreadsheet or a statistical package like SPSS to do the calculations for her. The statistics, and how she interprets them, will tell her things like how much diversity is in a stream, how polluted it is, or how healthy its fish populations are.
She will then write a paper that tells other scientists--or, at times, government officials, what she has found out. The paper is peer-reviewed (reviewed by other biologists) and often published in a journal. These days, papers are often published on the Internet as well. The biologist might go to a conference, too, to give a presentation.
Once the biologist has published his findings, his paper becomes a resource for other biologists who are trying to form hypotheses. So you can see, scientific research is like constructing a tall building--or a whole city, really. Each published paper is a building block or beam on which someone else can build. This is why it's critical that each study be done well, each piece of data be accurate, and each scientist be impartial. Even so, biologists might later discover that an important part of a building is defective.
Links about studying streams and riversMacroinvertebrate links
To learn more about studying streams, check out the reading list, where you will find texts, guides, and manuals suitable for all levels of knowledge and experience. (You will be able to order them from here, too).
To learn how you can help monitor a stream in your own watershed, contact your local ecology or environmental agency (usually to be found in the county or state sections of your telephone book). Many of the employees of these agencies also list their emails on agency websites.
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Taxa present in streams (and fish parasites)
One can't select the rocks one measures, of course, because if we did that we would tend to select larger rocks. A good system to use is to reach down and pick up the rock that is touching the very end of your boot.
Stream rocks can be classified according to the following scheme:
Boulder (125 cm or more)
Small Boulder (25-124 cm)
Large Cobble (15-24 cm)
Cobble (5-14 cm)
Gravel (2-5 cm)
Small Gravel (0.1-2 cm)
Sand (less than 0.1 cm and grainy)
Silt (less than 0.1 cm and floury)
Just like on a tree stump, if you see many rings that are thin, and close together, they will make a dark band. If you see rings that are thick and far apart, they will look light by comparison. These dark and light bands are what one uses to read fish scales.
The scale is compressed, and placed under a microscope or other viewing device. The biologist adds one light band to one dark band--which would mean a full year of one summer and one winter--and calls it a year. In this way, the biologist can tell how old the fish was that the scale came from.
It might be obvious to you that in parts of the world where there are no seasons, like toward the equator, it is nearly impossible to determine the age of a fish in this fashion!
Why do we use Latin names for things? It's a dead language, after all. Why don't we just call them by the names everyone knows? And who cares about all those phylums and classes and orders and the rest?
The way we classify organisms today all began with Carl von Linne, a medical doctor and botanist from Sweden otherwise known as Linnaeus. In his day (the 1700's), people were already using Latin to name things, because at the time it was considered to be the language of the truly educated. The trouble was, there was no system. The names were all different, and some of them were ridiculously long.
The system that Linnaeus invented used just two words to describe any organism: its genus and its species. A genus described a group of related organisms, and a species described only one organism. It was the first time anyone had used a hierarchy to describe organisms, and it was really much easier.
Because it made everything so much easier, scientists extended the hierarchy, trying to make everything alive fit into its own place on a tree of life, so to speak. At the very top, there are Kingdoms. Animals go into one of the kingdoms. Then, Phylums, Classes, Orders, Families, Genuses, and finally Species. Each one of these constitutes a taxon (the singular form of taxa). For instance, Kingdom Animalia is a taxon. A phylum beneath it, Chordata (the vertebrates), is also a taxon. A class beneath that, Mammalia (mammals), is a taxon, too. You can tell when you are looking at genus and species names, because they are always underlined or in italics.
The hierarchies help us learn about living things. When a thing is in its correct place on the tree, knowing where it is on the tree gives us information about it. It is like knowing what people are like in your region, in your state, in your city, in your neighborhood, and in your family.
The tree keeps changing. Besides the taxa listed above, scientists have added many more. They change the names of taxa, too, and often can't agree on what group should go in what taxa. Even genus and species names get changed. This is not a bad thing. It's a sign that progress is being made.
Even though Latin is a dead language today, it is the language that has been used by biologists, botanists, doctors, and other scientists for several centuries. It's just to late to change it! It's easiest to just keep training scientists in the Latin names. Otherwise, old journals and books would be indecipherable. The good news is that an elementary course in Latin can really help you to understand the names and make them quite easy.
Macroinvertebrates (living organisms that have no backbones but are large enough to be seen) include mites, clams, snails, worms, crustaceans, insects, and insect larvae and pupae. Though these are all very tiny, they make up a huge part of any stream community. They are a food source for fishes, which is one reason they are important. Another reason is that they have become a very popular means of determining the health of streams.
Biologists have developed biotic indices that tell them how healthy a stream is. When they use benthic organisms--macroinvertebrates--to do this, the indices are called B-IBI's (benthic indices of biotic integrity). All they have to do is collect, identify, and count macroinvertebrates (MI's), then plug the numbers they get into formulae. The reason this works so well is because some MI's are more sensitive than others to pollution. Some can tolerate only the cleanest, most natural waters (they are sensitive). Some can live in just about anything. And others fall inbetween somewhere. Volunteer stream monitors quickly learn which species are sensitive.
One popular index is the EPT, which uses only three orders of insects: Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies). It's popular because it's fast. Others indices use nearly everything that is collected.
The links below will provide you with more information about how to develop and use B-IBI's. They are PDF documents, so you will have to have Adobe Reader to read them! 
Stream Biological Assessments (Benthic Macroinvertebrates) for Watershed Analysis/Mid-Sol Duc Water, 1998, Robert W. Plotnikoff, Washington State Department of Ecology, Pub. 99-334.
Using Invertebrates to Assess the Quality of Washington Streams and to describe Biological Expectations, 1997, R. W. Plotnikoff and S. I. Ehinger, Washington State Department of Ecology, Pub. 97-332.
Instream Biological Assessment Monitoring Protocols: Benthic Macroinvertebrates, 1994, R. W. Plotnikoff, Washington State Department of Ecology, Pub. 94-113.