Common Biological Measures
Benthic macroinvertebrates are frequently used as a biological water quality indicator because they are abundant, easier to capture than fish, and because they are easier to identify than algae or protozoans. Macroinvertebrate samples can be collected using a Hess sampler in larger (fifth and sixth-order) streams or a Surber sampler in smaller streams. Macroinvertebrates are identified and enumerated, and the number of organisms at each site is estimated from the average of three same size sample areas. Benthic macroinvertebrate densities are reported as the total number of organisms per square meter of stream bottom. In addition to the total number of those organisms, measures of diversity particularly at the taxonomic level of order such as mayflies, stoneflies, beetles, and other organisms should also be noted. The Shannon index and the EPT index measure the diversity and quality of an invertebrate community respectively.

Common Chemical Measures
Assessment of water quality by chemical measures includes measures of various elements and molecules dissolved or suspended in water. Chemical measures commonly used in water-quality field surveys can reveal an imbalance within the ecosystem. For instance, pH identifies acid/base balance of water. Low pH values (indicating acidity) are particularly useful for detecting acid mine drainage. However, since some streams are naturally acidic, a low pH does not necessarily indicate acid mine drainage. Conversely, in systems with high alkalinity--a measure of the water's ability to buffer or resist changes in pH--normal pH values may not rule out the presence of acidmine drainage.

The level of nitrates in a body of water is another chemical measure of water quality. Nitrogen exists in water in numerous forms, two of which are nitrate (NO₃) and nitrite (NO₂). Of these two forms, nitrate is usually the most important. Nitrate is an essential nutrient for growth of algae and other aquatic plants, and can be present at high levels due to a variety of sources. Nitrate is very difficult to measure directly. A common procedure is to first measure the level of nitrite and then reduce the nitrate to nitrite and measure the combined nitrite concentration. Subtracting the original nitrite level from the combined nitrite concentration will give you the nitrate level. Nitrate measurements are reported as nitrate nitrogen (mg/L). Nitrite measurements are reported as nitrite nitrogen (mg/L).

Some chemical indicators are specific to particular forms of pollution. For instance, low dissolved oxygen often results from either the presence of raw sewage or acid mine drainage.

Other "chemical" measures are actually physical measurements that indicate the presence of chemicals in the water. For instance, conductivity--the ability to conduct an electrical current--is a physical measurement that indicates the presence of chemical ions in the water sample. For example, when table salt (NaCl, sodium chloride) dissolves in water, it forms ions (Na+ and Cl-) that allow a current of electricity to pass through the water. Water density is another physical measurement that indirectly indicates the presence of chemicals. The density of water is related to salt content (salinity) and water temperature. The salinity of a body of water is one of the main factors determining what organisms will be found there.

Common Physical Measures
A variety of methods exist to determine several physical characteristics of surface water within a given watershed:

• Stream order
• Catchment area (square kilometers)
• Built-up area (square kilometers)
• Percent built-up (percent)
• Elevation (meters)
• Water temperature(degrees Celcius)
• Air temperature( degrees Celcius)
• Stream width (meters)
• Average depth (meters)
• Maximum depth (meters)
• Minimum velocity (meters per second)
• Maximum velocity (meters per second)
• Average velocity (meters per second)
• Discharge [flow] (cubic meters per second)
• Forest canopy (percent shaded)
• Average rock size (diameter in centimeters)
• Maximum rock size (diameter in centimeters)
• Water transparency (Secchi disk or turbidity tube)

Some sites that address methods and tools to monitor and assess the quality of water resources:

• An Introduction to Water Quality Monitoring
• Estuary Monitoring
• Lake Monitoring
• GLOBE Water Quality Monitoring Protocols at a Glance
• The Watershed Project
• The EPA

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