The cyanobacterium Anabaena circinalis has the ability to co-produce geosmin and saxitoxins, compounds which can compromise the quality of drinking water. This study provides pertinent information in optimising water treatment practices for the removal of geosmin and saxitoxins. In particular, it demonstrates that pre-oxidation using potassium permanganate could be applied at the head of water treatment plants without releasing intracellular geosmin and saxitoxins from A. circinalis. Furthermore, powdered activated carbon (PAC) was shown to be an effective treatment barrier for the removal of extracellular (dissolved) geosmin and saxitoxins, with similar adsorption trends of both compounds. The relative removal of the saxitoxins compared with geosmin was determined to be 0.84±0.27, which implies that saxitoxin removal with PAC can be estimated to be approximately 60 to 100% of the removal of geosmin under equivalent conditions. Chlorine was shown to be effective for the oxidation of the saxitoxins with CT values of approximately 30 mg min l−1 required for greater than 90% destruction of the saxitoxins.