Cylindrospermopsis raciborskii is a commonly encountered cyanobacterium (blue-green algae) found in water bodies worldwide, particularly tropical and subtropical lakes and reservoirs. The changing global climate, increasing eutrophication from agricultural runoff and other factors are contributing to an increased occurrence of this alga in lakes and reservoirs worldwide, with blooms now also reported in temperate areas. Blooms pose a serious concern for water managers, since C. raciborskii growth is often accompanied by production of the toxin, cylindrospermopsin (CYN). This toxin clearly represents a human health concern but also targets a range of aquatic plants and animals. In recent years, research into the potential risks associated with CYN contamination of human drinking water supplies has grown considerably. However, by comparison, few studies have examined the potential for, and the influences on, ecological (environmental) effects associated with toxin-producing blooms. Consequently, whilst the World Health Organisation is working towards a provisional guideline for CYN in drinking water, the environmental management of toxic blooms remains underdeveloped: ecological risks appear to be poorly recognised, evaluated or minimised. This chapter will review the current research available on the toxicity and bioaccumulation of toxin from C. raciborskii, with a focus on managing the environmental toxicity of blooms. Aspects including algal growth dynamics, toxin production, modes of exposure in the aquatic environment, influences on uptake routes and potential for toxic metabolism and bioaccumulation in target organisms are discussed. Furthermore, to address the gap in environmental research concerning CYN, a summary of recent, laboratory-based ecotoxicity studies is given. Finally, a model to calculate the ecological risks associated with Cylindrospermopsis blooms is provided: this involves a consideration of cell concentrations, toxin concentrations and the relative proportions of cell-bound and aqueous toxin. This chapter is designed to raise awareness of the potential ecological effects associated with C. raciborskii in lakes and reservoirs worldwide, and to stimulate further work towards the development of ecologically relevant guidelines for toxic blooms in affected water bodies.