Temperature: The temperature of stream water is influenced by both natural processes and human activities. Climatic zone, altitude, air temperature, and season of the year produce variation in water temperature. Other natural factors include shade provided by streamside vegetation, depth, flow rate, snow melt, and mixing with ground water.  Human activities also introduce thermal pollution into streams through industrial discharge, stormwater warmed by urban surfaces, and removal of trees and tall vegetation that provided shade.

Thermal stress and even shock can occur when the temperature changes more than 1 or 2C in less than 24 hours. In addition, the sensitivity of an aquatic organism to toxic wastes, parasites, and disease often increases with rising temperatures.

Water temperature affects the amount of dissolved oxygen and other gases that water can hold at specific atmospheric pressure. A rise in temperature decreases the ability of water to hold oxygen molecules.

Dissolved Oxygen: There are two main sources of dissolved oxygen in stream water: the atmosphere and photosynthesis. Waves and tumbling water mix air into the water where oxygen readily dissolves until saturation occurs. Oxygen is also introduced by aquatic plants and algae as a byproduct of photosynthesis. One measure of dissolved oxygen in water is parts per million (ppm), which is the number of oxygen molecules (O2) per million total molecules in a sample.  The amount of dissolved oxygen is limited by physical conditions, such as water temperature and atmospheric pressure.

Lower temperature ---> higher potential dissolved oxygen level

Higher temperature ---> lower potential dissolved oxygen level

Oxygen is essential for fish, invertebrate, plant, and aerobic bacteria respiration. Dissolved oxygen levels below 3 parts per million (ppm) are stressful to most aquatic organisms. Levels below 2 or 1 ppm will not support fish. Fish growth and activity usually require 5-6 ppm of dissolved oxygen.

pH: The pH of a liquid is the negative logarithm of the concentration of hydrogen ions in the solution.  The concentration of carbonates (CO42-, HCO31-) and carbon dioxide (CO2(aq)) is the main influence on the pH of clean water. High concentrations produce alkaline waters (high pH), while low concentrations usually produce acidic waters (low pH).

The pH of natural water depends on several factors: the carbonate system, types of rock, types of soil, and nature of discharged pollutants.

The pH values of natural surface waters usually range from 5.5 to 8.5. Extremely high (9.6) and low (4.5) values are unsuitable for most aquatic organisms. Young fish and immature stages of aquatic insects are extremely sensitive to pH levels below 5.

Changes in pH can also affect aquatic life indirectly by altering other aspects of water chemistry. Low pH levels accelerate the release of heavy metals from sediments on the stream bottom. The heavy metals can accumulate on the gills of fish, reducing their chance of survival.

Turbidity: This is the measure of the relative cloudiness of water. Turbidity is caused by suspended solid matter scattering light as it passes through water. Suspended solids include clay, silt, plankton, industrial waste, and sewage. Soil erosion introduces soil and mineral particles to surface water. Stream bed sediments can be stirred up by organisms feeding off the bottom. Particles remain suspended by water currents for some time. Urban runoff introduces a wide variety of particles to stream water. Algal growth from added nutrients and sunlight can also increase turbidity.

As the amount of suspended solids increases, photosynthesis decreases, fish gills become clogged, and eggs are smothered. Material settling into spaces between rocks makes these microhabitats unsuitable for the macroinvertebrates living there. Surface water temperature also rises as suspended particles near the surface absorb heat from the sunlight, which in turn affects dissolved oxygen levels.

Another concern of suspended sediments is that attached nutrients, metals, and pesticides can be carried throughout the water system.

Hardness: Water hardness is a historical term referring primarily to the amount of calcium and magnesium ions present. Calcium and magnesium enter the stream mainly through the weathering of rocks.  A stream's hardness reflects the geology of the catchment area and provides a measure of the influence of human activity in a watershed. Calcium is an important component of plant cell walls and the shells and bones of many aquatic organisms, while magnesium is an essential nutrient for plants and a component of the chlorophyll cycle. Waters with calcium levels of 10 ppm or less usually support only sparse plant and animal life.

When the total hardness of water exceeds the total alkalinity, the excess is called "noncarbonate hardness" and indicates the presence of chloride and sulfate ions.

Alkalinity: The buffering capacity of water is measured as the "alkalinity." Alkalinity does not refer to pH, but instead refers to the ability of the water to resist change in pH. A total alkalinity level of 100-200 ppm will stabilize the pH level in a stream. Levels of 20-200 ppm are typical of fresh water. Levels below 10 ppm indicate that the system is poorly buffered. Poorly buffered waters are susceptible to changes in pH from natural and anthropogenic (human-caused) sources.

Conductivity: The ability of an aqueous solution to carry an electric current is called conductivity. The current is conducted in the solution by the movement of ions. Conductivity increases with increasing amounts and mobility of ions. In natural water, the dissociation of inorganic compounds is the main source of ions in the solution. Therefore, measuring conductivity reveals the concentration of dissolved salts in water. Conductivity is also affected by heavy metal ions released into water by acid mine drainage.

Total Solids: This is the sum of dissolved and suspended solids.

The quantity of dissolved material is mainly determined by the solubility of rocks and soils that the water contacts. Water that flows through limestone and gypsum dissolves calcium, carbonates, and sulfates, resulting in high total dissolved solid levels. The amount of material dissolved in a water sample affects its ability to conduct electricity. Total dissolved solids can be estimated by measuring conductivity, because as total solids increase, conductivity also increases.

Runoff from urban areas can carry salt from streets, fertilizers from lawns, along with other types of materials to contribute dissolved solids. Wastewater treatment plants can add phosphorus, nitrogen, and organic matter. Leaves and other plant materials dumped into streams are another source of dissolved solids. Soil particles are introduced by soil erosion and runoff. Decayed plant and animal matter is naturally converted to particulate matter within the water.

High concentrations of total solids can lower water quality and cause water balance problems for individual organisms. Low concentrations may limit the growth of different aquatic life. High concentrations of dissolved solids can lead to laxative effects and unpleasant mineral taste in drinking water.

Fecal Coliform: These are bacteria that are naturally abundant in the lower intestines of humans and other warm-blooded animals. Their presence serves as a reliable indication of sewage or fecal contamination in water. Fecal coliform can enter water through various sources, including mammal and bird discharge, agricultural and storm runoff, and human sewage discharge.

Biological oxygen demand: (BOD) is the measure of the amount of oxygen consumed by microorganisms in aerobic oxidation of organic material. Unpolluted natural waters will have a BOD of 5 mg/L or less.

The organic matter available for decomposition has both natural and human origins. Nutrients are the main culprit for high BOD in river water. Calm stretches of water ways also collect organic wastes that settle out from upstream. Swamps, bogs, and vegetation along the water provide organic matter for decomposition.

Chemical oxidation of sulfides, ferrous ions, and ammonia introduced to the stream through human activities also consumes oxygen in water.

Nitrates: Nitrogen is an element needed by all plants and animals to build protein. It most commonly exists in its molecular form (N2) where it is unusable for most aquatic plant growth. Blue-green algae converts N2 to ammonia (NH4+1) and nitrate (NO3-1) that can be taken in and utilized by aquatic plants. Ammonia is also released as bacteria break down aquatic plant and animal remains. Specialized bacteria can then oxidize the ammonia to form nitrites (NO) and nitrates (NO3-1).

Excretions of aquatic organisms are very rich in ammonia. In large groups, duck and geese can contribute heavy loads.

Nitrogen in the forms of ammonia and nitrates functions as a plant nutrient.

Sewage is the main source of human-influenced nitrate addition to streams. Nitrates are introduced by inadequately treated wastewater from sewage treatment plants, effluent from illegal sanitary sewer connections, and poorly functioning septic systems. Fertilizers from fields and runoff from cattle feedlots, dairies, and barnyards are other nitrate sources.

Total Phosphate: Phosphorus present in natural waters is usually found in the form of phosphates (PO4-3). Phosphates accumulate from living plants and animals, their byproducts, and their remains. Phosphate ions bonded to soil particles and in laundry detergents also end up in streams. Other sources of phosphorus include sewage, animal waste, soil erosion, fertilizers, and drained swamps and marshlands.

Phosphate acts as a "growth-limiting" factor of aquatic plants and algae. Excess phosphate creates blooms of extensive algal growth.

Phosphorus initially stimulates aquatic plant growth, which unlocks even more phosphorus from bottom sediments.  Algal blooms then become more frequent and further deplete the water of dissolved oxygen as the algae decays.

Eutrophication:  Eutrophication is an increase in the concentration of chemical nutrients in an ecosystem to an extent that increases the primary productivity resulting in negative environmental effects such as anoxia and severe reductions in water quality, fish, and other animal populations.