Background
Just as the stream transports energy upstream and down in the form of organisms and organic matter, it also transports nutrients. To an ecologist, nutrients are the elements, such as carbon or nitrogen, out of which organisms are built. More than a dozen different elements are important constituents of living things. Among the most important for aquatic ecosystems are nitrogen and phosphorous.
Nitrogen and phosphorus are particularly critical to aquatic ecosystems because they often control the rates of photosynthesis. This is not because nitrogen and phosphorous are the most abundant constituents of living things - carbon is significantly more abundant than either of them, and oxygen and sulfur are more abundant that phosphorous. Instead, it is because nitrogen and phosphorous are less available to plants relative to their growth requirements than are other elements.
One of the interesting dynamics of flowing water environments is that the directional flow of nutrients is almost always from upstream to downstream. Anadromous fish such as salmon, steelhead and shad that migrate back into freshwater headwaters from the ocean as adults are one of the few mechanisms to transfer large quantities of nutrients from the ocean to the mountains. The spawning of eggs and the death of individual fish provides organic material rich in nitrogen and phosphorus to oftentimes relatively nutrient-poor headwaters, which in turn benefits the biological production of those systems.
While there are many chemical constituents that are potentially important to freshwater ecosystems, nitrogen and phosphorus are particularly critical to rates of photosynthesis.
Phosphorus

Phosphorus is often in short supply in an aquatic ecosystem and limits plant and algae growth. The primary natural sources of phosphorus to aquatic ecosystems are the slow dissolution of minerals in soil and decomposition of allocthonous organic matter, such as leaf litter, although natural sources also include soil dusting and burning. But human activities have dramatically increased delivery of phosphorus to freshwaters. Primary anthropogenic sources of the nutrient include sewage (whether treated or not), septic tank leachate, fertilizer runoff, soil erosion, animal waste and industrial discharges.
Phosphorus in its most common forms such as orthophosphate, is not very soluble in water. Conversely, it adsorbs to clay particles well, reacts to form nearly insoluble precipitates with iron, aluminum and calcium. Most plants, algae and bacteria are capable of rapid uptake of the element, especially in the form of orthophosphate, when it is present even at low concentrations. Riparian forests and wetlands often efficiently trap phosphorous because they retain sediments, allow for uptake of the nutrient into aquatic and terrestrial plants, and provide opportunities for chemical reactions in the soil that can immobilize phosphorus.
While phosphorus is converted to different chemical forms in the phosphate cycle, plants readily use orthophosphate (PO4) and take up excess orthophosphate for storage. In lakes and ponds, dead material sinks to the bottom, where aerobic decomposition releases usable phosphorus, which is quickly used or becomes converted naturally to the less usable meta-phosphate. Meta-phosphate builds up in sediment, where under anaerobic conditions, can be converted back into the more usable orthophosphate form. Many aquatic plants, however, can use both forms.
Nitrogen
Nitrogen is a major constituent of all proteins, and thus of all living organisms. A lack of nitrogen can limit plant growth in both terrestrial and aquatic ecosystems. As with phosphorous, we often add nitrogen to farm fields and gardens in the form of fertilizers to increase production of crops and other desirable plants.
It may appear surprising that lack of nitrogen can limit growth of plants, since nearly three quarters of the atmosphere consists of nitrogen gas, N2. How can plants bathed in nitrogen not have enough nitrogen to grow? The answer lies in the complex chemistry of nitrogen.
Nitrogen gas, N2, is chemically very stable. The N-N molecule is linked together by a strong triple covalent bond. It takes a considerable investment in energy, just the right chemical environment, and some catalytic tricks to break the N-N triple bond and free elemental nitrogen to support growth. Only a few groups of organisms can carry out the process, which is known as nitrogen fixation. Today, the ability is found in cyanobacteria (blue-green algae), some bacteria like the Rhizobium that live symbiotically in the root nodules of legumes, and fungus of the genus Frankia, that live symbiotically with alders and a few other shrubs.
Nitrogen has a more complex biogeochemistry that phosphorus, in large part because nitrogen chemistry is closely linked to energy metabolism of microorganisms. Nitrogen takes many chemical forms in the environment, the most important of which are ammonium, nitrate, nitrite, organic nitrogen, and nitrogen gas. Nitrogen is interconverted among these forms by biochemical processes mediated by microorganisms in the environment (see figure below). For example, nitrogen fixation readily occurs in freshwater. When nitrogen availability limits plant or algae growth in freshwater ecosystems, populations of nitrogen fixing organisms (especially cyanobacteria) increase until some other nutrient - often phosphorus - becomes limiting. Because nitrogen fixation is less rapid in marine environments, nitrogen is more likely to limit primary production in marine and estuarine environments than in freshwater. Nitrogen can be limiting in phosphorus-rich environments.
The Aquatic Nitrogen Cycle
The primary natural source of nitrogen to aquatic and terrestrial ecosystems is biological nitrogen fixation; smaller quantities of nitrogen are fixed chemically by lightning and as a byproduct of natural combustion. As is true of phosphorous, human activity has dramatically altered the nitrogen cycle. Some estimates suggest that human activity has now more than doubled the rate at which atmospheric nitrogen is converted to bioavailable forms such as ammonium and nitrate. Plants and diatoms (a type of algae characterized by a silica shell) prefer ammomium and nitrate. Increases in these forms of nitrogen from sewage, fertilizer, and animal waste typically cause plant and algae production to ramp up, leading to longer term fluctuations in dissolved oxygen that may limit sensitive fish and aquatic life. Large quantities of nitrogen are fixed industrially to produce fertilizer, high temperature combustion in everything from automobile engines to power plants produces significant nitrogen, and widespread cultivation of nitrogen fixing crops such as alfalfa and soybeans also increases nitrogen flux. Human activities have in fact profoundly altered nutrient levels in many of the world's surface waters through sources named above. Globally, total dissolved nitrogen and phosphorus have doubled. In western Europe and North America, levels have increased by factors of 10 to 50.
Excess Nutrients in Aquatic Environments
An increase in nitrogen and/or phosphorus (in particular) in stream or lake environment can lead to a process called eutrophication that is especially apparent in lake environments. Eutrophication (Wikipedia definition) is a natural process in lakes that occurs as lakes gradually fill in with organic material over geologic time and waters become increasingly shallow and warm. Lakes and streams may also undergo anthropogenic eutrophication, where human inputs of nutrients create excessive algal blooms and result in decreased water clarity and dissolved oxygen. See Manitoba research on eutrophication.
In lakes, ponds and some near-shore marine ecosystems, increased nutrients lead to over-production of organic matter, primarily by phytoplankton. As the excess organic matter settles towards the bottom, it decomposes, consuming available oxygen, and liberating nutrients to fuel yet more production. The consumption of oxygen can quickly use up available oxygen, leaving large volumes of water without sufficient oxygen to support most aquatic life. This results in fish kills, mortality of benthic organisms like aquatic insects and shellfish, and loss of fish habitat.
Similar effects occur in rivers and streams, although the most severe effects are somewhat less common because flowing waters tend to be shallow and vertically well mixed, increasing the flow of oxygen into the water column by diffusion from the atmosphere. These facts make flowing water ecosystems more resistant to the most severe effects of excess nutrients. Nevertheless, excess nutrient inputs can and do degrade flowing water ecosystems. For example, phosphorous entering the Meduxnekeag River in Maine from a local sewage treatment plant leads to growth of extensive filamentous algae in the river during the late summer, when river flows are at their annual lows and water temperatures at annual maximums. The filamentous mat itself impedes vertical mixing of the water, so dissolved oxygen concentrations can drop to very low levels, forcing trout and other fishes to migrate out of affected reaches or die.
In aquatic ecosystems, it is important to recognize that there are healthy ranges all of these aspects of water chemistry, including water temperature, dissolved oxygen, pH and nutrients. If too little of one of these components is available, the ecosystem will suffer, just as it will if there is too much of another.
In stream systems, the concentration of nutrients is a strong indicator of the overall health of the stream. This is in part because excess nutrients directly degrade stream ecosystems, and also because of the processes by which nutrients enter streams. While atmospheric deposition of nitrogen (see Acid Deposition Threat) can be important even in remote locations, most excess nutrients entering streams come from human activities upstream. Whether excess nutrients are derived from failing septic tanks, ineffective sewage treatment plants, poorly managed agricultural practices, or land clearing for subdivision construction, the presence of excess nutrients is often an indicator of other, more fundamental problems in the watershed. As an example, since phosphorus often binds to sediments, high phosphorus concentrations in a stream may be a symptom of increases streambank erosion and sedimentation, which may in turn be caused by an increase in stream power that result from increased impervious surfaces.
Further Reading:
Phosphorus link
USGS - Reducing Phosphorus Pollution
NYS Attorney General - Phosphorus Report
Ecology Society of America
Allen, J. David. 2001. Stream Ecology. Norwell, Massachusetts: Kluwer Academic Publications.
Caduto, Michael J. 1990. Pond and Brook: A Guide to Nature in Freshwater Environment. University Press of New England.
Schlesinger, W. H. 1997. Biogeochemistry: An Analysis of Global Change. Academic Press, New York. (ISBN 0-12-625155-X). A classic college to graduate-level text on all things related to movement of nutrients in ecosystems.