A stream is a combination of all of its physical, chemical and biological characteristics. Human activities shape and alter many of these characteristics. The health of our rivers and streams is closely linked to their surrounding watersheds. Ecologists measure the extent to which human activities affect watershed health by gathering and recording information on physical conditions, water quality and living communities in streams and in the surrounding environment. The long-term stream monitoring program meets the requirements of state and federal regulations and supports the Board of Supervisors' environmental improvement program by providing an ongoing evaluation of the streams. The program maintains a substantial database, which over time will be used to determine the overall rate of change or trends in the conditions of our waterways.
The bacterium Escherichia coli (E. coli) is used as the water quality indicator for fecal contamination in surface water. Grab samples of water are collected seasonally to determine the concentration of E. coli in our streams. Based on the levels of E. coli found, we discourage swimming in natural waters. See 
These diverse organisms have varying tolerances of nonpoint source pollutants such as toxins, excess nutrients and sediment, making them well suited as indicators for determining stream health and water quality. They are picked out of the vegetative debris and identified to the genus taxonomic level.
A healthy and diverse fish community is indicative of good stream health. A backpack electrofisher unit is used to send electricity into the water to momentarily stuns the fish and allow for easy collection. Once collected, the fish are identified to the species taxonomic level and counted to track their populations. The fish are then released back into the water.
Stream habitat incorporates the physical, chemical and biological components that influence the structure and function of the aquatic community. It is visually assessed and scored for features, such as how much of the stream bottom is affected by sediment, what percentage of the stream bank is covered by native vegetation, the frequency of riffles and bank stability.