Part of ensuring healthy aquatic ecosystems and safe water in Canada involves measuring water quality by collecting and testing samples. This is known as monitoring.

Monitoring helps us to assess the safety of water for human uses, as well as the safety of lakes and rivers for plants, fish, and wildlife. Water samples, whether taken from the source (e.g., lake or river) or from the tap, can be tested for a variety of physical, chemical, and biological characteristics.

Some measurements can be made directly at the lake or river, such as temperature, pH (acidity), dissolved oxygen or suspended materials. Samples are sent back to the laboratory for more complex chemical measurements, such as for metals, nutrients (e.g., from fertilizers), pesticides and other substances. Biological testing may be done for microbiological pathogens, such as bacteria, viruses and other microscopic life that can lead to disease and illness. Biological indicators, such as benthic invertebrates, can also be used to assess water quality.

The types of measurements taken vary depending on the goals of the monitoring program or the type of information sought.

Monitoring information is used to help scientists and water managers determine if substances in water are at safe levels compared to water quality guidelines. When monitoring is done over a period of months or years, it can show if water quality is improving or deteriorating. This can help us know if pollution prevention, treatment and clean-up programs are working.

In Canada, water quality monitoring is carried out within partnerships amongst provincial, territorial, and federal governments, municipalities, universities, water associations, environmental groups and volunteers. In general, provinces conduct much of the water quality monitoring within their boundaries. The federal government's monitoring focuses on inter-provincial and international boundary waters (e.g., Great Lakes) and other areas of federal authority (i.e., Territories, National Parks, and other federal lands). Monitoring of recreational waters is generally carried out by local municipalities. Monitoring of tap water, delivered through municipal supply systems, is also usually undertaken by local municipalities, often in partnership with provincial agencies.

The Prairie Provinces Water Board has developed an active water quality program on eastward flowing interprovincial rivers, since 1974.

In 2006, CCME released "A Canada-wide Framework for Water Quality Monitoring". The purpose of the Framework is to enhance water resource management by serving as a guide to jurisdictions in the development and implementation of water quality monitoring programs in Canada.