Over the past decade, effect-based monitoring (EBM) has been increasingly applied for water quality monitoring. Despite being recommended as a monitoring tool in several guideline documents, the use of EBM remains limited to research projects. This study aimed to review the bioanalytical data published from studies conducted on wastewater, drinking water or reuse and to identify knowledge gaps and priorities for action. The results provide an overview of the biological effects associated with raw and treated waters, the reduction of these effects by treatment and a comparison of the detected response with effect-based trigger values. This review highlights a lack of data for many biological effects and the need to more thoroughly investigate effects such as aryl hydrocarbon receptor agonism, genotoxicity and oxidative stress. The results show that most drinking water schemes effectively eliminate the biological effects associated with environmental micropollutants. However, the oxidative stress response and genotoxicity, likely related to formed disinfection by-products, deserve closer attention since they seem to represent a higher concern in drinking water than any other effect. Overall, existing wastewater treatment schemes are less effective in removing biological effects, and consequently, priority should be given to the improvement of wastewater treatment for the better protection of the environment.