Freshwater systems contain about 10 % of the fauna species on earth and offer environmental services; however, human activities affect freshwater resources structurally and functionally, reducing the possibilities of using it. Thus, freshwater ecosystems are recognized as the most threatened worldwide, and therefore, aquatic organisms require attention for their conservation. Biological methods have proved to be suitable for the surveillance of aquatic ecosystems. In this sense, given their biological and ecological features, freshwater fish and macroinvertebrates, from the suborganismal to community level, exhibit excellent response signals to stressors. In this contribution, we review the main approaches for assessing freshwater ecosystems using fish and macroinvertebrates. At low organization levels, biomarkers are excellent early warning indicators making evident that organisms have been in contact with contaminants and the effects can be reversible, while the high organization levels reflect an overview of the global impact on aquatic resources; both organization levels show spatial (locally and regionally), and temporal (past and present) effects of water quality conditions of the aquatic ecosystems.