Monitoring of physicochemical parameters within freshwaters is essential to understanding possible triggers of algal blooms. One important parameter which is often overlooked is dissolved organic matter (DOM). DOM plays a major role in abiotic and biotic processes within aquatic ecosystems. Studies comparing the effect of different DOM at varying concentrations on the growth and toxin production of cyanobacteria, as well as the possible role of DOM in the development of harmful algal blooms, are currently limited. This study aimed to determine how different types of DOM affect the structure of phytoplankton communities. Changes in abundance of phytoplankton and community structure in Lake Hume water, collected from three different sites, in the presence and absence of 2 mg-C L-1 DOM were assessed using fourteen day bioassays. Two different types of DOM were used and differed in key characteristics such as source (allochthonous and/or autochthonous), aromaticity, abundance of key components such as proteins, humic and fulvic acids, and C/N ratio. The Type of DOM was shown to influence the abundance of the potentially toxic cyanobacteria Chrysosporum ovalisporum. Significantly higher cell counts were recorded in presence of the Appletree Creek DOM (AT) which is characterized as: humic rich; higher C/N ratio; dark colour; highly aromatic; high molecular weight; higher allochthonous molecules; lower protein-like substances. In contrast, a significant decrease in the number of cells of the same cyanobacteria was observed in the presence of the Minnamurra River DOM (MI) which is characterized as: fulvic-rich; lower C/N ratio; light colour; lower aromaticity; lower molecular weight; high autochthonous molecules; higher protein-like substances. Community structures also differed significantly between the two DOM treatments. This suggests that DOM may play an important role in either stimulating or inhibiting growth of harmful algae and influence the phytoplankton community structure.