The management of inland waterways to protect recreational users from cyanotoxin exposure is complicated by the common management practice of using proxy indicators of cyanotoxin production (cell counts and biovolumes of potentially toxin species), rather than the cyanotoxin itself. This widely accepted practice is further complicated by a lack of advisory guidelines for non-microcystin-producing cyanotoxins. This study has investigated the effectiveness of this management approach over five and a half years, monitoring 65 different sites in South East Queensland using phycological and toxin-analysis. This study concluded that cell counts of Cylindrospermopsis raciborskii, the most common potentially toxin producing species of cyanobacteria in South East Queensland's inland lakes, was a poor proxy indicator for cylindrospermopsin toxin production. Seqwater, the local water authority responsible for the management of recreational access to drinking water storage lakes, initiated an alternative management approach for recreational cyanobacterial water quality management in December 2016. This new approach is based on cyanobacterial toxin guideline values for five different cyanotoxins, with closures and warning notices issued based on the actual cyanotoxin concentration, not the proxy indicator. We encourage other recreational water management authorities consider this approach to manage recreational access in the future.