The role of trace metal micronutrients in limiting cyanobacterial growth and structuring the phytoplankton community is becoming more evident. However, little is known regarding the extent of micronutrient limitation in freshwaters or which micronutrient conditions favour potentially-toxic cyanobacteria. To assess how freshwater phytoplankton respond to micronutrient and macronutrient additions, we conducted nutrient amendment bioassays at seven sites across South Eastern-Australia. Sites were variable in cyanobacterial cell densities and phytoplankton community compositions. At two sites, Mannus Lake and Burrendong Dam, micronutrient additions (iron, cobalt, copper, manganese, molybdenum and zinc) increased cyanobacterial growth, indicating micronutrient limitation. Both sites had cyanobacterial blooms present at the onset of the experiment, dominated by Chrysosporum ovalisporum at Mannus Lake and Microcystis aeruginosa at Burrendong Dam. This suggests that micronutrients may be an important regulator of the severity of cyanobacterial blooms and may become limiting when there is high competition for nutrient resources. The addition of the micronutrient mixture resulted in a higher proportion of cyanobacteria compared to the control and a lower diversity community compared to phosphorus additions, indicating that micronutrients can not only influence cyanobacterial biovolume but also their ability to dominate the phytoplankton community. This reinforces that micronutrient requirements of phytoplankton are often species specific. As micronutrient enrichment is often overlooked when assessing nutrient-constraints on cyanobacterial growth, this study provides valuable insight into the conditions that may influence cyanobacterial blooms and the potential contribution of micronutrients to eutrophication.