In most small streams and rivers, the seasonal pattern of water temperature, the first of these factors, is determined largely by the extent that direct solar radiation and air temperature can modify the temperature of the water. In a given region, groundwater stays fairly constant in temperature throughout the year (+-1 degree C of mean annual air temperature for the region) and provides most of the baseflow for stream systems. Loss of shade from streamside forests can greatly warm streams, increasing a trout's demand for dissolved oxygen and, at the same time, reducing the amount of dissolved oxygen available in the water.
Headwater streams of the first to third order comprise about 85% of the total length of running waters, and because of the ratio of stream bottom to shoreline, are most readily influenced by exposure to solar energy. Agricultural drainage systems which intercept cool groundwater and drain it to streams in unshaded ditches contribute significantly to the increase in stream temperature.
Manipulation of the streamside forest canopy can be used to moderate and stabilize stream temperature to optimize the survivorship, growth, and reproductive needs of fish and aquatic macro-invertebrates and even benthic algae.
Habitat structure, the second factor affecting Salmonid survival, is enhanced by the addition of the stream channel of large woody debris which forms pools and important rearing areas. This debris also provides cover from predators and protection from high flows.
To understand the third factor, food availability, the natural stream must be viewed as a continuum from headwaters to mouth with a significant amount of the energy for aquatic life coming from organic materials such as leaves, twigs, flowers, animals and insects originating from the streamside forest. These kinds of materials dominate the food base of small headwater streams flowing through the forests. The food supports a diverse invertebrate community which, in turn, provides the principal food source for Salmonids in healthy ecosystems. Large amounts of leaf litters and other organic matter enter forested headwater streams and are rapidly consumed by aquatic invertebrates. These animals function as shredders because they reduce large pieces of organic debris to smaller pieces which move downstream and can be used by other animals who feed by filtering or gathering these fine particles of food.
As stream channels get wider in a downstream direction, the widening partition between the streamside forest canopies allows sufficient light to promote the growth of benthic algae, especially diatoms. Many species of invertebrates known collectively as "grazers" specialize in eating diatoms and, in turn, provide important food for fish. In large rivers that are very wide and deep, plantonic algae can become the dominant food resource with forest litter being less important.
The downstream changes in channel size and shape and the organic food base along the river continuum greatly affect the fish population. For example, fish populations change from invertebrate-eating Salmonid fishes, such as trout and salmon, in the headwaters to plankton-feeding Cyprinids and Catostomids, such as carp and suckers, in large rivers.
Streamside forests facilitate the downstream flow of food by contributing large stable debris to the streambed. This stable debris is the mechanism by which the detritus is held long enough to be processed by the invertebrate community. Without debris dams, much of the organic input from streamside vegetation would be washed downstream without contributing to the life processes of the aquatic food chain. Only as the streamside forest nears maturity, is it able to produce organic debris in sufficient size and quantity to provide relatively stable detritus catchments.
The streamside forest helps to control sediment flux, the fourth factor affecting Salmonid survival, by stabilizing streambanks. Sediment concentrations must be very high (above 20,000 ppm) to cause mortality in adult fish by clogging the gill filaments and preventing normal water circulation and aeration of the blood. However, abrasion damage to gills begins to occur at sediment concentrations as low as 200 ppm.
In addition, low concentrations can cause behavioral changes and disrupt normal reproduction by converting spawning grounds and preventing the emergence of recently hatched fry. Sediment covering spawning grounds reduces the flow of intragravel water, limiting oxygen availability to incubating eggs and newly-hatched alevins and hindering removal of metabolic wastes. It similarly affects aquatic insect habitat, thus altering species composition of a major trout food source. Large instream debris can help store sediment, moderating transport rates and buffering against rapid changes in sediment loads that could cover spawning gravels, fill rearing pools and reduce invertebrate populations.