* Ephemeroptera 
* Plecoptera 
* Mollusca
* Trichoptera
* Escherichia coli (E. coli)
* Coliform bacteria
* Pimephales promelas (fathead minnow)
* Americamysis bahia (Mysid shrimp)
* Sea urchin
* Protists, e.g. Paratrimastix pyriformis
Biological monitoring metrics have been developed in many places, and one widely used family of measurements for freshwater is the presence and abundance of members of the insect orders Ephemeroptera, Plecoptera and Trichoptera (EPT) (of benthic macroinvertebrates whose common names are, respectively, mayfly, stonefly and caddisfly). EPT indexes will naturally vary from region to region, but generally, within a region, the greater the number of taxa from these orders, the better the water quality. Organisations in the United States, such as EPA. offer guidance on developing a monitoring program and identifying members of these and other aquatic insect orders. Many US wastewater dischargers (e.g., factories, power plants, refineries, mines, municipal sewage treatment plants) are required to conduct periodic whole effluent toxicity (WET) tests.
Individuals interested in monitoring water quality who cannot afford or manage lab scale analysis can also use biological indicators to get a general reading of water quality. One example is the IOWATER volunteer water monitoring program of Iowa, which includes an EPT indicator key.
Bivalve molluscs are largely used as bioindicators to monitor the health of aquatic environments in both fresh water and the marine environments. Their population status or structure, physiology, behaviour or the level of contamination with elements or compounds can indicate the state of contamination status of the ecosystem. They are particularly useful since they are sessile so that they are representative of the environment where they are sampled or placed. A typical project is the U.S. Mussel Watch Programme, but today they are used worldwide.
The Southern African Scoring System (SASS) method is a biological water quality monitoring system based on the presence of benthic macroinvertebrates (EPT). The SASS aquatic biomonitoring tool has been refined over the past 30 years and is now on the fifth version (SASS5) which has been specifically modified in accordance with international standards, namely the ISO/IEC 17025 protocol. The SASS5 method is used by the South African Department of Water Affairs as a standard method for River Health Assessment, which feeds the national River Health Programme and the national Rivers Database.