Biofilms can be regarded as early warning systems for detection of the effects of toxicants on aquatic systems, because they have been successfully used for detection of other environmental stressors (e.g. pH, salinity, organic pollution). A variety of methods is used for detection of the effects of toxicants by use of biofilms. The methods range from structurally-based to functionally-based, and from in vitro-based to systemic approaches. Physiological approaches may be appropriate for detection of acute effects. Among these methods, photosynthesis is more related to the effect of toxicants affecting algal communities, directly or indirectly, and extracellular enzyme activity is less specific. Selecting one or the other may depend on the suspected direct effect of the toxicant. Integrated studies have revealed the relevance of toxicants to top-down or bottom-up regulation of the biofilm community. Persistent or chronic effects should affect other biofilm indicators, for example growth or biomass-related factors (e.g. chlorophyll), or community composition. Among these, community composition might better reflect the effects of the toxicant(s), because this may cause a shift from a sensitive to a progressively tolerant community. Community composition-based approaches do not usually adequately reflect cause-effect relationships and require complementary analysis of properties affected in the short-term, for example physiological properties. The current array of methods available must be wisely combined to disentangle the effects of chemicals on biofilms, and whether these effects are transient or persistent, to successfully translate the chemical action of toxicants into the effect they might have on the river ecosystem.