Toxins produced by cyanoprokaryotes are a key issue in aquatic management because of their potential to exert adverse effects on humans and aquatic biota. The information gap regarding bioaccumulation and biomagnification processes associated with cyanotoxins, however, has resulted in inadequacies in the management and maintenance of biological diversity in lakes and reservoirs affected by toxic cyanoprokaryote blooms. This paper examines the potential for, and effects of, bioaccumulation of two common cyanotoxins, microcystin and cylindrospermopsin, in aquatic organisms. The factors influencing cyanotoxin bioavailability are discussed in the context of the challenges associated with understanding and managing toxin accumulation. Based on the characteristics of cyanotoxin bioavailability, exposure and uptake routes, a theoretical, predictive model for cyanotoxin bioaccumulation is proposed. Key concepts include monitoring changes in toxin availability throughout the progression of a toxic bloom and the prediction of ecological effects based on internal tissue concentrations. The model explores the minimum requirements that managers must undertake in order to properly assess bioaccumulation risk in terms of frequency of toxin testing, toxin fraction determination and assessment of aquatic organisms.