Do you mean to ask how we can assess the impact of human activities on freshwater ecosystems? Apart from monitoring physical/chemical characteristics, you would use bio-indicators (specific biological processes, species or communities) to get an idea on the ecological status of a certain water body.
If you mean to ask how to do an environmental risk assessment of chemicals (i.e., preferably before they enter the environment), there is a whole battery of standardised ecotoxicological tests that should be conducted. I am not familiar with the entire process but, typically, exposure tests to different concentrations of a single compound are performed to capture a variety of data on the toxicological responses of (model) organisms (e.g., LC50-values). These tests are performed on at least three species, each from a different trophic level. For instance: microalgae (primary producers), water fleas (primary consumers) and fish (secondary consumers). For each of these levels, a battery of standard test guidelines exists - which tests need to be performed will depend on the physicochemical properties of the compound. Such guidelines are made available by the OECD in Europe, and by the EPA in the USA - so this could give you some further lead. The data of such ecotoxicological tests will then feed into further analyses to determine what would be 'safe concentrations' in the environment. Typically, rigorous safety margins around those values will be used before defining environmental norms of a chemical.
Living in a country with way too many lakes and rivers to monitor, our first step is to do a risk analysis of potential impacts using land use and other pressures (hydropower plants). Areas at risk are then given high priority for monitoring/surveys.