Human activities in river catchments interfere with natural fluxes of water and materials. Diffuse inputs and point-sources of toxicants have modified the ecological state of riverine communities considerably, and sanitation schemes are now under development for various rivers. To improve analysis, monitoring and prospecting the role of toxicants in river ecosystems a review of the available methods is undertaken. Ecotoxicological techniques are discussed in relation to basic ecological principles that are thought to regulate the functioning of communities. The response to toxicants among species is highly diverse and therefore the choice of test species (e.g. of typical riverine insects as caddisflies or mayflies) is critical, as it is the use of test-batteries. Long-term exposure may lead to developmental disturbances that may be assessed through morphometric techniques like analysis of asymmetry. Multi-generation exposure, although rarely studied, provides a useful insight into the genetic consequences of pollution. Selection for tolerant species or varieties has been experimentally assessed for smaller organisms such as insects, micro-algae, and bacteria. There is also perspective for multivariate analysis of species distribution in relation to pollutant exposure. Furthermore, a system approach to benthic ecology and sediment testing is needed. Such an approach reflects the strong linkage of ecological and ecotoxicological processes. Toxicants are transformed by biological activity; in some cases this alleviates toxicant stress, but in other cases degradation products are toxic as well. The risk of transformation to mutagenic products in the environment is indicated. The re-assessment of some of the classical ecotoxicological techniques is needed to adequately fulfil the needs of ecological recovery programs. To this purpose integration of ecotoxicological and ecological tools is needed.