Abstract Many of the toxic substances entering freshwaters today are those which were present several decades ago, but others have become significant recently. The effects of toxicants in flowing waters are modified by unidirectional transport and dispersion which afford the potential for a degree of ‘self-purification’. The chemical quality of the receiving water also affects toxicity. Biological factors also contribute to the ultimate effect of pollutants. The potential for accumulation of toxic substances within tissues increases the significance of certain pollutants which may be present in water even though ambient concentrations are very low. The biota of flowing waters may be restored, following catastrophic entry of pollutants, by drift from unaffected regions upstream. The range of potential toxic substances is very extensive and includes inorganic poisons, organic poisons, heavy metals, pesticides and PCBs. Metals, pesticides and PCBs have the greatest potential for bioaccumulation. Few generalisations can be made regarding the effects of toxic substances on the biota. Each species tends to respond to different toxicants in different ways and even at different stages in its life-history. Toxicity tests conducted under controlled laboratory conditions sometimes produce conflicting results: it is not then to be unexpected that field observations should sometimes vary widely. Determinations of toxicity in laboratory tests must be applied with caution to field conditions and it is not wise to extrapolate findings to other species or environments.