Since October 1997, 47 reservoirs and weir pools across tropical and subtropical Queensland have been regularly monitored for the occurrence of planktic cyanoprokaryotes. Cylindrospermopsis raciborskii (Woloszynska) Seenaya & Subba Raju (Nostocales, Cyanoprokaryota) was found in 70% of the storages, with one storage displaying year-round dominance, 50% of the reservoirs seasonally dominated and a seasonal presence in 46% of the weir pools. Maxima for the majority of storages occurred from late summer through to early autumn. The precise timing of onset of seasonal maxima varied considerably between storages and regions. Temperature and stratification patterns influenced seasonal recruitment with C. raciborskii reaching seasonal maxima in southern storages generally later than the northern storages. Overall peak seasonal abundance occurred in deep strongly stratified storages. The majority of storages experiencing concentrations > 15 000 cells mL–1 tested positive to the presence of the alkaloid cytotoxin, cylindrospermopsin. Median cylindrospermopsin concentration across the 14 reservoirs in which toxin was recorded was 3.4 μg L–1. The highest toxin concentrations were generally associated with storages in which C. raciborskii had been established for a considerable period of time, or occurred after the peak summer population maxima. Toxin concentrations of 1 μg L–1 were generally associated with cell concentrations of approximately 20 000 cells mL–1, hence this cell concentration threshold was adopted as a health trigger level at which to begin monitoring for toxicity. The morphology of this species was highly variable and included straight, coiled and sigmoid-shaped trichomes. Populations were routinely recorded as mixtures of all three morphotypes or proceeded as transitions from one morphotype to another throughout the year. The dominance of C. raciborskii appears to be favoured by a set of environmental and hydrological factors that include long water residence time, high pH, high temperature, high incident irradiation and a thermally stratified water column. The lack of visual monitoring cues, such as scum formation, variation in colour of the water body, rapid germination of large numbers of cells, highly variable morphology, relative toxicity and persistence of this species year round in many areas, continues to make this species a primary focus of water managers.