Nitrogen and phosphorus are critical nutrients required by most living organisms but excess levels of these elements can create problems. Nitrate is usually the most abundant form of nitrogen and is typically dissolved in water. High concentrations of nitrate can be harmful if consumed by warm-blooded animals, including humans, because nitrate (NO3-) can be converted to nitrite (NO2-) within the gastrointestinal tract and nitrite reacts with hemoglobin to limit oxygen transport in the blood. Excess nitrate can also stimulate algal blooms. Some species of algae excrete toxic waste products. Usually of more importance is that when the algae die, the processes of decay require oxygen and thus decrease the levels of dissolved oxygen in the river water.

Many rivers in industrialized countries now experience a one-two punch. The first punch comes from when substantially increased volumes of nitrogen enter the river corridor in runoff from artificially fertilized agricultural lands and effluent from urban wastewater treatment plants. The second punch is that channelization, floodplain drainage, and other modifications of the river corridor reduce the river ecosystem’s ability to biologically take up nitrogen. Microbial communities within the hyporheic zone and in riparian soil can take up excess nitrogen, but homogenizing and simplifying channels, and floodplain drainage and deforestation significantly reduce or destroy the environmental conditions that these microbial communities require to exist.

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