Glossary of Ecological Terms


Acid deposition - Acids (e.g., nitric and sulfuric) form as the result of burning fossil fuels and also emanate from various industrial sources (e.g., paper mills, steel mills). They volatilize into the air and accumulate on dust particles in the atmosphere. They eventually settle to the ground. Rain and snow bring down acid particles, as well. When precipitation of any kind forms in regions of heavy acid deposition, the acids are solublized and leach valuable minerals from the soil. Eventually, repeated leaching depletes the buffering capacity of the soil, with devastating effects on the wildlife that live in the streams draining these regions (see Heavy Metals and pH).     

Algal Bloom - An increased growth of algae (single-cell plants) in response to an increase in nutrients or pollutants, usually phosphates and nitrates from detergents and fertilizers. 

Allochthanous - This refers to the source of energy input to rivers and streams. The term means from outside the river (e.g., dead leaves, branches and dead trees that fall into the river). Most freestone rivers get their energy in this fashion.

Anadromous fishes - Any species of fish that lives as an adult in salt water and spawns in freshwater. For example, all salmonids, striped bass, and shad. 

Anchor Ice - ice that forms on the bottom of the river. It can cause great damage by trapping immature macroinvertebrates to the underside of rocks and killing them, thus lowering the energy flow into the secondary consumer group (e.g., trout, suckers, dace and other insect-eating predators). 

Arbor Day - A day set aside for tree planting. Each state has a specific time in the year for this purpose designated by the National Arbor Day Foundation (see Links). These dates are carefully chosen to correspond to the time of year most favorable for the survival of newly planted trees and shrubs and always fall on a Friday, thus allowing K-12 schools across the country the opportunity to participate in this useful activity.

Artesian aquifer - Artesian aquifers are associated with mountainous regions of the world. The water in this configuration (see also Confined aquifer) is under great pressure from the water above due to the gradient of gravity. This creates a hydrological situation resulting in a spring whenever the confined aquifer breaks through the impermeable rock layer and rises to ground level, allowing water to be pushed out onto the surface.       

Assemblage - A collection of plants or animals of the same taxa (e.g., order, family, genus) living within a common geographic locale, often in competition with one another for food, space, energy, etc..

Autochthanous - Sources of energy that come from within the river, itself. All spring and limestone streams and many tailwater rivers account for more than half of their annual energy budget from the macrophytes that grow in situ. Algal growth on the rock substrate in freestone rivers and streams represents another important in situ energy source.  

Aquifer - Geological strata (i.e., porous rock) that allows water to accumulate within it. It can be either confined or unconfined (see definitions for both).


Bacteria - Single cell organisms that possess cell walls and lack a definable nucleus for their DNA (i.e., prokaryotes). Bacteria are critical for the functioning of all ecosystems and are thus essential for the in-stream conversion of dead plant material into a form that macroinvertebrates find appetizing.

Basaltic Rock - Geological formations that began as volcanic lava flows. 

Benthic Zone - The bed of the river, stream or creek. Benthos is Greek for “bottom”.  

Biomass - The total amount of living material expressed as either grams of carbon or          kilocalories (1,000 calories) for a given area of space (e.g., per square meter). Kilocalories are calculated by placing together all of the living matter collected for a defined area of riverbed and drying it. After recording the total weight, it is then placed into a bomb calorimeter. The calorimeter is filled with pure oxygen and a spark ignites the contents. The amount of heat given off is recorded in calories per gram of dried material. 

Bioproductivity - The total amount of living material (number of organisms or kilocalories/m2) a given area of river can produce (see Biomass) within a prescribedperiod of time (usually one calendar year). Often, this measurement is in terms of a specific type of aquatic life form (e.g., macrophyte, macroinvertebrate, fish).

Boreal Forest - Circumpolar northern pine forests.


Caddis fly - Insects in the Order Trichoptera. The order name means “hair wing” in Latin. There are 15 sub-orders with over 5,000 species, and 1,200 live in streams throughout North America. They are particularly abundant in most trout streamsthroughout the world. Caddis flies are some of the most important members of the macroinvertebrate community that make up the food webs of most rivers and streams. They undergo complete metamorphosis (egg - larva - pupa - adult fly). Most are filter-feeders, while some are entomophagus (i.e., insects that eat other insects).    

Calcium carbonate - This is the main component of limestone. Calcium is an essential ingredient of the macroinvertebrate exoskeleton. This compound dissolves in weak acid, dissociating into Ca (2+) and (-) CO3. In doing so, it makes calcium available to the life forms of the stream, and at the same time changes the overall pH of the environment to slightly basic in pH (typically 7.2-7.8). These are the two reasons why limestone streams are so productive. 

Calorie - A unit of heat energy. The amount of heat needed to increase the temperature of 1 gram of water by one degree centigrade. I prefer the definition an old medical entomologist friend of mine gave me when I was in graduate school. He said that a calorie was equal to that amount of energy we spend lifting a single mosquito one centimeter above a surface. Ecologists tend to express their data as kilocalories whenever convenient.  

Catadromous fishes - Any fish species that lives in freshwater and spawns in salt water. For example, the American eel lives as adult fish in rivers along the east coast of the United States, and spawns in the Sargasso Sea off the coast of Florida.

Catchment basin – geological formation that drains all lotic systems into a common river (see: Watershed)

Channelization- The straightening of a river by removing meanders, ostensibly for the        purpose of flood control. Usually, bulldozers and other heavy equipment are used. Channelization destroys the benthos and hyporrheic zones, as well as the riparian ecotone. Disconnecting the communities of life forms of the river by short-circuiting the flow of energy through each trophic level is the end result. Recovery is protracted, depending upon the extent to which the banks were altered. The Kissimee River in Florida, for example, remained straightened for many years after extensive channelization by the Corp of Army Engineers. Today, that river is scheduled to be routed to its original riverbed because studies have shown that the altered river had too great an effect on natural processes in the everglades. Many other smaller rivers throughout the world suffer from channelization each year.

Community - A mix of different taxa of plants and animals living in a common geographic region, through which energy flows, thus linking them into an ecosystem.

Competition - The vying for common resources (energy, space, etc.) in a given environment among individual organisms. This activity is one of the major biological forces regulating the structure and composition of macroinvertebrate communities on the benthos of most rivers.  

Confined Aquifer - Water that is trapped in a layer of permeable rock lying between two layers of impermeable rock is referred to as a confined aquifer. It is under great hydrological pressure and often results in an artesian spring (see Artesian Aquifer).

Crustacean - Any organism in the Phylum Arthropoda, Class Crustacea. This diverse group includes crabs, lobsters, crawfish and amphipods (scuds) among others. The latter two groups are often found in limestone streams in high abundance and contribute significantly to the food chains and food webs of that river type.

Current - Movement of water down a gradient of gravity. Current is measured as flow in feet per minute. The scientific notation Q=AV is a mathematical expression of current, where Q is the current, and A is the cross sectional area of the river at any given point along its course, times the velocity - V - of the water flowing passed a fixed point on the bank.


Defoliation - The act of removing plant life from a given region. Elimination of plants from along the riparian ecotone of freestone rivers significantly detracts from the            bioproductivity of those aquatic ecosystems.

Delta - An alluvial deposit of silt from a large river system at the level of the estuary.

Detritus - Dead plant and animal material. Detritus is reduced to small particles by  microbial decay and shredder macroinvertebrates in most rivers. Re-cycling of detritus constitutes the base of the energy flow pyramid from plants to top carnivores in most freshwater aquatic and terrestrial ecosystems.   

Developmental Cycle - The complex biological process through which all living organisms go in order to complete their life cycle. Macroinvertebrates complete their transformation from egg to adult employing two separate strategies; namely incomplete(egg - nymph - adult = mayflies and stone flies) or complete metamorphosis (egg - larva - pupa - adult = caddis flies and all diptera).     

Diptera - Insects with two wings (di=two,  aptera= wing). Included in the diptera are           mosquitoes, house flies, deer flies and black flies. Midges, mosquitos, black flies and deer flies are aquatic insects that are found in abundance in some freestone rivers.   

Dissolved Oxygen - Gaseous oxygen comprises 21% of the total gas in the atmosphere at sea level. It is very soluble in water and the amount that can dissolve in it depends upon two physical parameters: pressure and temperature. By far, temperature is the most important one regarding rivers, since the atmospheric pressure at sea level is about the same for the water in a river as the land around it. Trout and macroinvertebrates require an ideal concentration of 6-10 milligrams of dissolved oxygen per 1,000 milliliters of water. At higher altitudes, reduced atmospheric pressure becomes important, especially for alpine situations where the amount of oxygen in the    atmosphere is reduced and the pressure is also lower. However, the colder temperatures compensate for these changes, for the most part.     

Drawdown - The release of water from an impoundment controlled by a valve system attached to the top or bottom of the dam.    

Drift - This macroinvertebrate behavior is keyed to the day/night cycle and is referred to as a diurnal rhythm. Many species of arthropods participate in the drift each night during the summer months. Typically, organisms emerge up into the water column at two distinct times during the night; the first at about 1 hour after dark and the second at 4-6 am. They drift downstream until they reach the bottom of the pool in which they reside. As morning approaches, they migrate long the bottom of the river back to their original place of lift off. The purpose of drift is still being investigated.


Ecology - Derived from the Greek word “Oikos”, it translates into English loosely as ”Living together in the same house”. Today, we understand the word ecology to stand for the science of how disparate groups of organisms cooperate and compete in a common geographic region to create interdependencies that we call ecosystems. This definition still falls far short of fully describing the breadth and depth of ecological sciences, but its not too bad a working definition.    

Ecological modeling - The quantitative science in which computer-assisted mathematics and related software programs are employed to describe complex processes of nature (atmospheric modeling, predator-prey relationships, climate change models, etc.). Most ecological models take into account extensive physical, chemical, and biological data and apply them to a variety of levels of interactions.    

Ecosystem - Most ecologists will not commit themselves to defining just what it is that constitutes an ecosystem. So for our purposes, I will simply characterize an ecosystem as being comprised of communities of a wide variety of assemblages of plants and animals sharing a common geographic region. They display a set of complex interactions between them allowing energy flow to proceed upward along the food webs and food chains. This activity links all those life forms into interdependencies. Most of the energy remains within the communities and re-cycles again and again, unless disturbed from the outside by extreme environmental change.  

Ecosystem Management - The almost impossible task of insuring that ecosystem services are functional in regions impacted by the presence of human activities. This newly coined phrase is still undergoing field testing. We have yet to “get it right”, but we continue to try. To manage an ecosystem, we must understand how it works, and that is the crux of the problem facing the next generation. 

Ecotone - The edge of two or more ecosystems. For example, the two banks of the river, the interface between the woods and an open field, a hedge row next to a field, the meeting of freshwater with salt water (i.e., estuary), etc. This zone is a region of high biodiversity and attracts plants and animals to it that cannot usually be found in any of the bordering ecosystems. For this reason, alone the ecotone is a valued (albeit small) piece of real estate.

Eddy - A slowing down of or reversal of current in a river, usually caused by the obstruction of the main flow by a large object such as a rock, fallen tree or sand bar. Eddies are resting places for fish and large amounts of detritus collect there at certain times of the year.  

Energy Flow - The transfer of energy (i.e., calories) from one set of organisms to another by the ingestion of biologically produced material. There are typically four trophic levels through which energy passes in an ecosystem: 1. Primary producers (plants) fix energy from the sun into new plant tissue; 2. Primary consumers eat plants; 3. Secondary consumers eat herbivores; and 4. Tertiary consumers (ie. top carnivores) eat secondary consumers. 5. Animals at every trophic level die periodically and the nutrients they represent are re-cycled by detritivores (ie. shredder macroinvertebrates and microbes like bacteria and fungi), or are consumed by scavengers that also die. In-ground nutrients are used by the primary producers. Its a tightly connected cycle when it functions unhampered by outside influences. Unavoidably, parasitism and intra- and inter-specific competition conspire to reduce the efficiency of the ecosystem.

Encroachment - Disturbing natural systems by activities such as construction of housing, shopping malls, clear-cut harvesting of forest products, farming, dam building, etc.     

Essential Nutrient - An element or compound absolutely necessary for the life of a given organism. For example, humans need a minimum of 11 kinds of amino acids and two kinds of fatty acids, as well as numerous other nutrients for normal growth and development. Macroinvertebrates need calcium, nitrates and phosphorous, as well as numerous other essential nutrients.    

Estuary - An aquatic ecotone between the river and the ocean.

Eutrophic - Environments enriched in essential nutrients from natural and human sources (pollutants such as detergents, fertilizers, etc.). This situation allows for uncontrolled growth of algae in aquatic ecosystems, particularly in standing bodies of water, resulting in oxygen depletion.   

Evolution - Biological change over geologic time through the process of natural selection.

Exoskeleton - The outer hard “shell” of all arthropods (i.e., insects, arachnids, crustacea, etc.).


Feeder Stream- A small tributary of the main stem of a river system.

Fertilizer - There are two kinds of fertilizers: 1. Synthetic mixtures of agrochemicals enriched in elements and compounds not found in abundance in natural systems. These manufactured products unavoidably contain trace elements that can accumulate to higher concentrations if the product is used frequently. Such is the case in the Imperial Valley of California where selenium, a trace element, is now found in the water table in some places at toxic levels for waterfowl. 2. Natural fertilizers include manures from various animal sources and composted non-edible portions of plants.   

Filter Feeder - An organism that obtains all of its food in the form of fine particulate organic matter (FPOM). Many species of macroinvertebrates in the river are filter feeders. Many possess specialized organs for doing so. For example, brush-like hairs around the mouth and forelegs facilitate this kind of feeding behavior in the Isonychia, a mayfly genus. Other species of Ephemeroptera employ intricate nest-building in the sandy      deposits behind rocks, while most Trichoptera (caddis flies) build webs to trap FPOM. Clams, oysters, and a wide variety of coral reef organisms also feed in this fashion 

Food Chain - A linear expression of the flow of energy in a given situation in which the     number of different kinds of organisms involved are few. For example, sunlight, grass, cow, or: sunlight, algae, minnows, trout (lake food chain).

Food Web - An expression of the flow of energy through various communities of organisms in ecosystems typically consisting of four or more trophic levels. Food webs dissipate energy, spreading it out laterally to communities of organisms living at the same trophic level. Most stream and river ecosystems are comprised of food webs, not food chains. For example, sunlight, in-stream macrophytes, macroinvertebrates, trout and other insect-eating fishes, predators of trout. Many macroinvertebrate and fish species feed on in stream insects, thus taking away from the flow of energy towards the top trophic levels.    

Fragmented Ecosystem- An ecosystem that has been encroached upon in such a way as to create two or more smaller regions, as is the case when logging roads are made through portions of forest, canals are dug separating land regions, or major highways are constructed, severing a wildlife refuge into two parts. Fragmentation is occurring at a rapid rate, as humans seek to expand their living spaces to include wild areas near rivers, streams and creeks. Maintaining green belts along riparian ways is an enlightened developmental approach to help avoid fragmentation.  

Freestone River - A river in a mountainous area whose sources of water include snow melt and a series of coalescing springs. The benthic zone is strewn with smooth rocks, boulders, gravel and sand. Few macrophytes grow there due to the steep gradients and swift currents that characterize this river type. Macroinvertebrate communities typically form food webs, and productivity is modest, compared to limestone streams, due to the slightly acidic pH of the water and the swiftness of the currents 

Fungus - Any organism in the Kingdom Mychota. These organisms do not carry out           photosynthesis, so they derive all their food from either dead or living plants and animals. Some fungal species are parasitic, while most are saprophytic (those that consume dead things, only), and these organisms are essential detritivores for the world’s rivers and rain forests. Many aquatic fungi or water molds (hyphomycetes) participate in the breakdown of leaf and other plant materials in freestone rivers. They are essential, along with bacteria, for making the decaying vegetation palatable for the macroinvertebrate shredder species.


Genus - A level of taxonomic classification that immediately precedes species

Gradient - An expression of the variability of physical, chemical, and biological properties of a given ecosystem. There is a gradient created by the river as it cascades down the mountain side. In this instance, current speed, daily fluctuations in water temperature, the amount of dissolved oxygen, pH, suspended particulates, macroinvertebrate communities, fish species and other characteristics of the freestone river are distributed along the gradient of gravity.   

Granite - A type of ancient (billions of years old), very hard, crystalline rock formation whose origins were solidified portions of molten crust of the earth.

Groundwater - Water located in porous rock below the surface of the earth in either confined or unconfined aquifers. Most limestone rivers begin as groundwater springs. 


Habitat - The physical space occupied by a plant or animal. Not to be confused with niche.  

Hardwood Forest - Any forest in which the dominant species of trees are deciduous, such as oak, maple, beech, ash, etc.. These forests are essential for the flow of energy into most of the world’s freestone rivers.

Heavy Metal - Rock music aside, heavy metals include tin, lead, gold, platinum, selenium, mercury, cadmium, vanadium, iron, nickel, silver, and cobalt. Many of these are toxic in greater than trace amounts, but toxicity (usually expressed as the amount of a given substance needed to kill 50% of a population of organism, or LD50) varies with the tolerance limits for each organism. Most of these elements are contaminants from mining operations, smelting the ore, or industrial waste.  Other metals can also present problems for trout. For example, aluminum is extremely toxic at rather low levels (100 parts per billion), especially when calcium is in short supply. Aluminum is an abundant element in soil and becomes a problem in rivers receiving acid water, as occurs in the Spring throughout the North Eastern United States in the form of acid snow melt.     

Herbicide - Any agrochemical used to eliminate unwanted plant growth. Most are highly specific for plant species, but some are generally toxic for most plants and for many animal species, as well. Indiscriminant use of herbicides in agricultural settings has resulted in toxic situations for neighboring rivers during times of runoff, as might occur after a heavy rain storm or in the Spring when snow melt runoff is common.  

Herbivore - Any animal that predominantly eats plants. Almost all animals will take a bite of meat now and then, so there are few strict herbivores in nature

Hydrological Cycle - Water falls to earth as rain and becomes included in the groundwater (see Aquifer), or runs into standing bodies of water, where it remains for some time thereafter. Eventually most of the surface water returns to the oceans via rivers, where it evaporates and condenses forming clouds. Cycles of cloud formation, rain and terrestrial runoff characterize the hydrological cycle. Groundwater, on the other hand, can take centuries to exit from the aquifer and return to the oceans. The same is true for water that is trapped as snow in the polar regions. Only about 2% of all the freshwater on earth is in liquid form, and 20% of that is in Lake Baikal, Russia. More and more, the remaining 80% of liquid freshwater is becoming polluted.   

Hyphomycetes- Water molds (see Fungi) that are important for the re-cycling of energy into aquatic ecosystems. The breakdown of leaf material in the freestone river is dependent on this group of fungi. There is a unique succession of species of hyphomycetes that colonize different species of leaves that make characterizing this detritivore activity extremely difficult. 

Hyporheic Zone - The region of a river that typically starts at the benthic zone and goes downward until groundwater from the river is no longer included in the substrate. This is a relatively new zone for ecological study, and its physical, chemical and biological characteristics for any river have yet to be fully investigated. It is strongly suspected that this poorly oxygenated zone serves as a reservoir for stream life, particularly arthropods, at times of drought, flood and other environmental stress. Channelization destroys this zone, along with the benthic zone, as well.  


Impoundment - Any standing body of water created by a dam.

In situ - A Latin word denoting within. For example, macrophytes grow in situ in limestone streams. 


Karst systems – referring to streams that erode their way through limestone deposits

Keystone Species - A plant or animal the removal of which causes a rearrangement of energy flow relationships to occur within that ecosystem. In one classic experiment, excluding the top carnivore, the steelhead trout (Onchorynchus mykiss), from a portion of freestone river by placing wire baskets over portions of the benthos, resulted in a collapse of the balance between herbivorous macroinvertebrates, insectivorous fishes, such as the stickleback, and the top carnivores. Sticklebacks are favorite food items for steelhead and eliminating the possibility for predation resulted in the sticklebacks consuming all herbivorous insects within the confines of the basket. As the result, an overgrowth of filamentous algae occurred within the area of the basket. In this instance, the steelhead trout was the keystone species. Therefore, over harvesting predator species in riverain ecosystems results in energy flow rearrangements the outcome of which does not usually favor that environment as trout habitat. In limestone streams, the scud (crustacean amphipod) is a keystone species, as is most macrophytes. 


Leaching - The chemical process by which elements (eg. sodium, calcium, aluminum, etc.)  are selectively dissolved out of the solid substrate of the river bed or stream bank. Leaching occurs under slightly acid conditions. This is the reason no two rivers are the same, since leaching is responsible for the chemical composition of the water. When organic matter falls into the river, especially leaves, leaching occurs allowing soluble substances such as sugars, plant pigments and other organics to enter the water column. The input of these plant-derived materials in the Fall triggers the growth of microbes that prepare the leaf surface for the shredder species of macroinvertebrates. In regions where acid deposition and precipitation is the rule (e.g., Northeastern United States), seasonal leaching of heavy metals, primarily aluminum, into the river causes the death of countless fish and macroinvertebrates. Coal and gold mining operations have left acidic and arsenic compounds in the slag heaps that occasional leach into rivers and despoil them for long periods of time.       

Lentic – referring to standing bodies of water (e.g., lakes)

Limestone Stream - A moving body of water characterized by a low gradient riparian zone, a slightly basic pH, slow currents, in situ  macrophytes, cold water, and a high rate of bioproductivity.

Lotic – referring to rivers


Macroinvertebrate - Any arthropod (e.g., Order Diptera, Coleoptrea, Trichoptera, Ephemeroptera, Plecoptera) or Gastropod (snail) species living within the confines of the river. These communities of animals form complex food web associations, and typically occupy the second and third trophic levels for most of the world’s cold running water ecosystems

Macrophyte - Any species of large vascular plant living within slow moving rivers. Mostly found in limestone and spring creeks, and large warm water rivers.  

Mainstem - The final section of river, below which cannot be found any tributaries larger in volume than itself. 

Mayfly - All species of macroinvertebrates in the Order Ephemeroptera. There are             2,000(+) species world-wide, and 620(+) species in North America and Mexico

Meander - The winding of a river back and forth within its banks. Erosional activity of moving water creates meanders and the precise number of switch backs from left to right looking downstream depends upon the width of the river, the speed of the current and the substrate over which the river flows (see Luna Leopold, “A View of the River” for an excellent analysis of the physics of meandering). In very large rivers, ox bow lakes are a common feature of the landscape due to severe meandering and periodic floods that cut off the meander with deposits of soil between the loops of river, creating a standing body of water in the process. In most freestone rivers, meanders are common, while in limestone situations, meanders are less predicable and may not be a regular feature, due to slow currents and low volumes of water.


Niche - The niche is a theoretical concept first fully developed by G. E. Hutchinson, and brought forward by numerous other distinguished ecologists. It attempts to define all physical, chemical and biological factors that influence a single organism throughout its life. Energy consumption is also part of the complex equation defining the “essential” niche. This global concept cannot be tested by experimental approach, yet it is a useful notion when considering the interactions of all life forms within a given ecosystem. The statement that no two organisms can occupy the same niche suggests that competition plays a significant role in the interactions between assemblages and communities of organisms. Defining the essential niche of any macroinvertebrate is an impossible task, considering its constantly changing environment. This fact, alone adds to the romance and mystery of river ecology.   

“No Kill” stretch - A portion of a trout stream in which all fish hooked and landed must then be returned back to the water as quickly as possible. This mode of fishing has gained in popularity over the last decade and is now the rule for many stretches of rivers across the country, throughout most of Europe, parts of South America, New Zealand and Australia. No kill fishing helps preserve the balance between prey and predator in the riverain ecosystem (see Keystone species).

Nutrient Loading - The entering of excess nutrients into a river, thus de-regulating the limiting factors controlling the bioproductivity of that system. Nutrient loading can be from natural sources, such as is the case for the Green River in northern Utah. Rich deposits of nitrates and phosphates, locked in the rock of the mountains above the normal level of the river were flooded by the impoundment created by the Flaming Gorge Dam project. As the result, these nutrients leached into the lake, producing huge algal blooms much of which was exported to the river below. The Green River below Flaming Gorge Dam is now one of the world’s greatest producers of trout per linear mile, because nutrient loading takes place in a cold water environment. Similar results occurred with the damming of the Madison River in Montana, and numerous other impoundments, as well. Negative effects on the growth of macroinvertebrates and trout are experienced when nutrient loading produces the wrong kinds of algae, namely blue-green species, or occurs in warm water situations in which algal blooms literally smothering the life forms by depleting the already limited amounts of oxygen during periods of darkness.


Oligothrophic- A term applied to lakes that are cold water bodies most of the year and which are nutrient poor. These lakes usually have a low biodiversity index, but can accumulate and support large populations of fish that have longevity built into their genetics. For example, some lake trout (Salvelinas namaycush) in Great Slave Lake innorthern Canada are over fifty years old.


Pesticide - Any synthetic or natural product that has deleterious effects against arthropods of various species. Many plants produce pesticide-like molecules as a defense against insects. The world’s agroindustrial community has produced a multitude of chemical compounds that work against various biological functions of arthropods. Organophosphates (DDT and the like) are the most widely known of these, and the mis-use of this one compound has caused much environmental change over the past 50 years. One of the major problems with the indiscriminant use of pesticides is their penchant for concentrating up the food chain and into the food webs of aquatic ecosystems, devastating macroinvertebrate communities in the process. This can occur because they are relatively long lived, making their removal from the environment protracted and difficult, at best.    

pH - A measure of acidity of a liquid. Formally defined, it is the negative log (base 10) of the hydrogen ion concentration. pH is expressed as a whole number on a scale ranging from 1 through 14, with 1 the most acid, 7 neutral, and 14 the most basic. Most rain water falls at a pH of around 6.8 due to the presence of small amounts of naturally occurring sulfuric acid. Buffering capacity of the ground (i.e., basic compounds that leach out as rain falls) converts rain water to a neutral pH.  Acid deposition from industrial sources and automobile exhaust fumes (nitric and sulfuric acids) help to accelerate the consumption of the soil’s buffer compounds. Another effect of acid leaching is the removal of most divalent metals (e.g., calcium, magnesium, molybdenum), leaving the trivalent metal aluminum in the soil. Eventually when all other buffer compounds are leached out, aluminum, too is mobilized, creating highly toxic events in trout streams in those regions. In northern and central Sweden and Norway, thousands of lakes are sterile because they lack an outlet and the land around those bodies of water has no neutralization capacity any longer. The same thing has happened in the Adirondack lakes of northern New York State. Remediation involves neutralizing substances like marble (pure calcium carbonate) chips being dumped into rivers and lakes in the hope that leaching will help to restore the pH back to normal.     

Photic zone - The surface of water through which light penetrates and stimulates the growth of photosynthetic plants (phytoplankton). This term is usually reserved for discussions of lakes and oceans, since most rivers that support trout are transparent, allowing light to reach all the way to the benthic zone.  

Pioneer Species- The first species of plants to emerge after clear-cutting or after a natural disaster such as tornado, flood or severe drought. These are shade intolerant organisms. 

Plankton - Any kind of microscopic aquatic organism, either plant (phytoplankton) or animal (zooplankton). Plankton are mostly consumed by lake dwelling filter feeders (eg. minnows), and filter feeding macroinvertebrate species of tailwater fisheries.

Pool - An erosional depression in the bed of a freestone river characterized by deep water, slow currents, and usually the presence of a spring hole.    

Predation - The act of one animal consuming another.   

Predator - Any animal that catches, then eats its prey. A member of the third or forth trophic level.

Primary Consumer - Any animal that eats plants on a regular basis. A member of the second trophic level.   

Primary Producer - Any plant with photosynthetic capacity


Remediation - The act of repairing a damaged portion of an ecosystem.

Resiliency - The ability of a damaged natural system to repair itself, if left alone. For example, clear-cutting all trees in a well-defined watershed, then leaving them lie in place was the basis for a simple yet important experiment in the Hubbard Brook watershed of New Hampshire conducted by Dr. Gene Likens. The trees were sprayed with a mild herbicide for three years after the initial cutting to discourage the growth of seedlings, and then the entire system was carefully monitored. It was demonstrated that the leaching of nutrients from unprotected soil was accelerated during the first three years, then returned to normal. During the first three years, pioneer species of plants grew out and provided shade for the shade tolerant tree species and held soil in place at the same time. These activities are referred to as ecosystem functions. Eventually the trees overshadowed the shade intolerant pioneer species and they died out leaving only the trees. The aquatic conditions of the Hubbard Brook returned to normal after the third year. Resiliency was the term used to describe these events. It was postulated that resiliency of the Hubbard Brook forest was due to a variety of factors not the least of which was the fact that tree seeds were long-lived in the soil and germinated after the clear-cutting. These studies give hope for other ecosystems damaged by the heavy hand of commercial logging. The intimate connection between river and forest cannot be emphasized enough.    

Riffle - A geological formation in a freestone river that is resistant to erosion resulting in shallow, fast flowing water. These regions precede pools, and together help to define the main flow characteristics of the freestone river.  

Riparian- Referring to the banks of rivers.

Runoff - Surface water that fails to seep into the ground. Runoff occurs when natural absorbers of water, "sponges" such as trees and shrubs have been removed from a given location. Runoff in suburban areas contains non-point source pollutants (gasoline, crank case oil, herbicides, pesticides, fertilizers, for example) that find their way into rivers and lakes. Often they drain into impoundments that are used for drinking purposes, raising serious issues of risk to human health.


Salmonid - Any fish species that is a member of the Family Salmonidae (see Appendix I).  

Secondary Consumer - Any animal that is a member of the second trophic level of an        ecosystem. Usually a predator or scavenger species.  

Shade Intolerant - Any plant species that cannot grow under shade conditions. Pioneer species typify this kind of plant.

Shade Tolerant - Any species of plant that can grow under shade conditions. Most tree species are shade tolerant, as are tropical plants that live below the canopy.

Shredder Invertebrate - Any species of aquatic arthropod that can process plant material by shredding it after it falls into the river. However, shredders need the detritus to be microbially processed first before they will take a bite. Shredders are sloppy eaters and send food particles downstream for a filter feeder feast.   

Siltation - The process of erosion in which portions of soil from the banks wash into the river. Silt covers macroinvertebrates and kills them. The single most important cause of siltation is the removal of trees from along the banks of the river

Species- A species is difficult to describe biologically except for those organisms that engage in sex. In those cases, their genetics, behavior, and geographic distribution defines the population. Geographic separation and/or the constant pressure exerted on it by mutations within that population leads to the eventual creation of new species by the process of natural selection, whereby the mutant best suited to its new environment stands the best chance of survival. The species concept is the lynch pin upon which the science of ecology is based.   

Spring Creek - A lotic ecosystem characterized by low flow rates of cold water that       emanate from a spring, and which harbors numerous macrophyte plant species. The pH of spring creeks vary widely, often approaching that of a limestone situation, but not infrequently reflecting conditions of most freestone rivers

Spring Hole - The emergence of an aquifer to the surface of the benthic or hyporheic zone of the river out of which flows cold, un-oxygenated water. Spring holes are refugia for trout and macroinvertebrates during periods of drought, floods and extreme cold when abundant anchor ice forms.  

Solar Constant - The amount of heat from the sun that strikes the surface of the earth each day expressed as calories per square centimeter of earth surface per minute. The actual amount is 1.94 cal/cm2/min. Recently, astronomers specializing in solar phenomena have discovered that this “constant” can and does change slightly from moment to moment, perhaps altering the energy budget for the planet and giving rise to small differences that might reflect themselves later in larger ecological changes.

Solar Radiation - The electromagnetic spectrum encompassing wave lengths in the light and heat range of frequencies arriving at the surface of the earth from the sun. The ozone layer in the stratosphere selects out certain ultraviolet frequencies, allowing the rest to pass onto the earth’s surface. Plants use light for photosynthesis in the visible blue-green region of the electromagnetic spectrum (i.e., 350-500 nanometers in wave length).

Stone fly - Any member of the Order Plecoptera. There are over 1,900 recognized species world-wide, with 595 species found in North America. Many are scrappers (i.e., algae eater), while others prefer to eat insects (entomophagus). They are among the oldest examples of aquatic insects and the first ones were without wings. Stone flies undergo incomplete metamorphosis (see Developmental cycle) and can take several years to mature in the stream before hatching.


Tailwater fishery -A river born at the base of a dam. These rivers are hard to characterize ecologically since their chemistries depend upon the impoundments above them. In general, they are highly productive, due to the relative constancy of environmental conditions (flow rates, annual temperature fluctuations, pH, nutrient input, etc.).

Tailrace - The portion of a tailwater river immediately adjacent to the dam. This area is usually where the highest water pressure is found. Because of this characteristic, it is also this region in which nitrogen saturation occurs. If fish are accidentally caught in the turbines of a power generating dam and forced through into the tailrace, they often suffer the “bends” and die. This routinely occurs in the West when the salmon fry attempt to negotiate the numerous dams on the Columbia River system in Washington State in their struggle to reach the ocean.

Teleost - Any member of the Class Osteichthyes. Teleosts are bony fishes, in contrast to sharks, skates and rays, which are cartilaginous fishes (Class Condrichthyes). 

Thermal Pollution - An upward change in water temperature exceeding the tolerance limits for aquatic life selected for life at lower temperatures. If no springs or feeder streams are available to offer temporary refuge from these events, a fish kill often ensues. Thermal pollution is the hallmark of tailwater fisheries not managed for the life forms in the river, but rather only for drinking or irrigation resources. Enlightened views on water release practices are gradually replacing such outdated thinking, and ecosystem management is the reason. 

Thermal Shock- The sudden release of cold or hot water into a river or stream. The effect is the same; namely severe disturbance of the life forms of that ecosystem.  

Tolerance Limit - The biological expression of an organism to live within certain prescribed physical, chemical, and biological parameters. For aquatic organisms living in cold, highly oxygenated water, the limits for life are defined by the amounts of dissolved oxygen, fluctuations in ambient temperature, and a variety of other related conditions that, taken together characterize the world’s trout rivers.  Exceeding a tolerance limit for any one factor effectively eliminates all organisms from that zone that share that characteristic. 

Trophic level - The word “trophic” is Greek, and is a term used to describe the flow of energy through a given ecosystem. In most ecosystems there are four trophic levels. The first is occupied by the primary producers, photosynthetic plants that convert a small portion of the incoming solar energy into edible biomass. The second is occupied by primary consumers that feed on plants. The third is occupied by the secondary consumers, and they feed on primary consumers, either by predation or scavenging dead animal carcasses. The final level, level four, is occupied by the top carnivores, and these predators feed on secondary and primary consumer groups, while some even feed on primary producers (e.g., the grizzly bear is mostly a herbivore, but you couldn’t tell that by looking at one!). The efficiency of the system is at about 10%. That is how much of the available energy is converted to biomass of the next trophic level. The rest, 90%, is dissipated as heat due to metabolism and respiration.


Unconfined Aquifer - Porous rock strata that contains water and lies above the impervious layer.  

Understory- Shrubs, wildflowers, and bushes that grow on the forest floor. Shade tolerant plant species. 


Watershed - A precisely defined geographic region through which drains a dendritic (i.e., bifurcating) pattern of rivers. All water falling on the watershed exits at the bottom of a single valley, usually as a full-fledged river, or flows into a lake that has an outlet allowing the river to resume its journey once the lake is full (see also: Catchment basin).