Toxic cyanobacterial blooms in urban lakes present serious health hazards to humans and animals and require effective management strategies. Managing such blooms requires a sufficient understanding of the controlling environmental factors. A range of them has been proposed in the literature as potential triggers for cyanobacterial biomass development and cyanotoxin (e.g. microcystin) production in freshwater systems. However, the environmental triggers of cyanobacteria and microcystin variability remain a subject of debate due to contrasting findings. This issue has raised the question of whether the relevance of environmental triggers may depend on site-specific combinations of environmental factors. In this study, we investigated the site-specificity of environmental triggers for cyanobacterial bloom and microcystin dynamics in three urban lakes in Western Australia. Our study suggests that cyanobacterial biomass, cyanobacterial dominance and cyanobacterial microcystin content variability were significantly correlated to phosphorus and iron concentrations. However, the correlations were different between lakes, thus suggesting a site-specific effect of these environmental factors. The discrepancies in the correlations could be explained by differences in local nutrient concentration. For instance, we found no correlation between cyanobacterial fraction and total phosphorous (TP) in the lake with the highest TP concentration, while correlations were significant and negative in the other two lakes. In addition, our study indicates that the difference of the correlation between total iron (TFe) and the cyanobacterial fraction between lakes might have been a consequence of differences in the cyanobacterial community structure, specifically the presence or absence of nitrogen-fixing species. In conclusion, our study suggests that identification of significant environmental factors under site-specific conditions is an important strategy to enhance successful outcomes in cyanobacterial bloom control measures.