Abstract In the past two decades, there has been an apparent increase in the frequency, intensity and geographical distribution of harmful algal blooms in Australian coastal, estuarine and fresh waters. Wild and cultured fish kills have been associated with blooms of the dinoflagellates Scrippsiella trochoidea (through the generation of anoxic conditions), Cochlodinium cf. helix, Gymnodinium cf. galatheanum, Gymnodinium mikimotoi and the golden-brown flagellate Prymnesium parvum (most likely through the production of substances affecting the gills of fish). Contamination of shellfish products with algal toxins has been caused by the diatoms Rhizosolenia cf. chunii (bitter-tasting compound), the dinoflagellates Alexandrium catenella, A. minutum and Gymnodinium catenatum (paralytic shellfish poisons) and, to a lesser extent, the dinoflagellates Dinophysis acuminata and D. fortii (diarrhetic shellfish poisons). Poisoning of cattle and wildlife or contamination of drinking water supplies by blue-green algal toxins from Nodularia spumigena (brackish water), Anabaena circinalis and Microcystis aeruginosa (freshwater) is also an increasing problem. The management of nutrient discharges to inland and coastal waterways is crucial to arrest the increasing impact of harmful algal blooms.