Human modification of landscapes and subsequent degradation of aquatic ecosystems is a global and deleterious threat to the ecological condition of waterways. Therefore, biomonitoring and bioassessment tools are needed that detect and evaluate change in aquatic environments quickly and reliably. Metabolomics is the quantification and characterization of small molecules, called metabolites, from normal processes within a cell, tissue or biofluid and has the potential to overcome weaknesses of tools used in current biomonitoring approaches. The use of metabolomics in bioassessments is rapidly increasing and it can evaluate how environmental stressors affect organism health and subsequently the condition of aquatic ecosystems. Here, I evaluate metabolomics as a biomonitoring and bioassessment tool and use several case studies to determine the performance and demonstrate the strengths of metabolomics for assessing aquatic ecosystem condition. Metabolomics met nearly all criteria of a good indicator of assigning ecological condition, is sensitive to environmental change, and can be an early-warning indicator of change in ecosystem condition. The results demonstrate that metabolomics could be adopted immediately as a powerful tool for conducting biomonitoring and bioassessments similar to current approaches. Moreover, metabolomic analysis of aquatic organisms holds great promise as an aquatic biomonitoring and bioassessment technique, as it is a sensitive, low cost and relatively quick method that managers can use to make more informed decisions of human impacts on aquatic ecosystem condition.