A review of the currently available literature—including studies dealing with toxicity assessment of both priority and emerging compounds—allowed the discussion of the pros and cons of their use as ecotoxicological endpoints in fluvial systems as well as their inclusion in regular monitoring programs.

Chlorophyll-a fluorescence measurements have the ability to detect effects of a large panel of chemical substances on the photosynthetic processes of fluvial biofilms, covering both functional and structural aspects of the biofilm community. Moreover, they might provide early warning signals of toxic effects.

Thus, the application of the chlorophyll-a fluorescence measurement is recommended as a complementary measurement of toxic stress in aquatic ecosystems. Their application is of special interest in the context of the Water Framework Directive (WFD, Directive 2000/60/EC), where the development of new structural and functional endpoints of the biological quality elements (e.g., biofilms) is required.