Abstract. This paper describes the vertical water column distribution of the cyanobacterial toxins cylindrospermopsin and deoxycylindrospermopsin in a water body containing the cyanobacteria Aphanizomenon ovalisporum and Cylindrospermopsisraciborskii. The study site was Cobaki Village Lake, a small stratified anthropogenic lake in north-eastern New South Wales, Australia. Water quality analysis indicated that stratification and oxygenation of the water column were significant in both the distribution of the cyanobacterial populations and their associated toxin concentrations. Toxin was distributed throughout the entire water column, but the highest concentrations were recorded in the hypolimnion. Maximum toxin concentrations were detected in February 2007 (38.2μgL−1 cylindrospermopsin (CYN) and 42.2μgL−1 deoxy-CYN). The relative distribution of CYN and deoxy-CYN paralleled the distribution of NH3H and NOX within the water column, with oxygenated chemical species dominating above 15m and de-oxygenated chemical species dominating below 15 m. Cyanobacterial cell concentrations were highest in the oxic, warm and low conductivity waters of the epilimnion and cyanobacterial species succession was associated with nutrient and trace-metal depletion in this surface layer. These research findings are directly relevant to the management of water supplies affected by toxic blue-green algal blooms, particularly with respect to the considered placement of off-take devices to avoid layers of cyanobacterial cell and toxin concentrations.