The indicator for algal blooms was assessed as “fair” for all lakes, due to the number of blooms in the past two decades (eight since 2001). Four of these were of the blue-green algae Nodularia, three were the blue-green algae Synechococcus and the bloom in the summer of 2015/16, was of the diatom Pseudo-nitzschia. The long-term record for algal blooms is incomplete and it is difficult to know if there is a trend in the frequency or extent of algal blooms in the system.

Extensive work has been conducted on the algal blooms and phytoplankton dynamics of the Gippsland Lakes (Webster et al. 2001, Grigg et al. 2004, Beardall 2008, Cook et al. 2008, Holland and Cook 2009, Holland et al. 2009, 2013a, 2013b, Day et al. 2011 among others). Conditions that lead to Nodularia blooms in the Gippsland Lakes are now relatively well understood (Day et al. 2011, Cook and Holland 2012).

In general, blooms of the blue-green algae occur when salinities are low, temperatures are high and the nitrogen is in short supply. Stratified conditions are also important as this facilitates the movement of phosphorus out of the sediments under the low oxygen conditions in the bottom waters, particularly in Lake Victoria. They also allow cyanobacteria to dominate over diatoms, as they can often regulate their buoyancy and thus position in the water-column, whereas diatoms, being heavier than water, tend to sink unless maintained in the water-column by periodic mixing. The environmental conditions for Nodularia blooms were identified by Cook and Holland (2012) as:

• Salinities between 9 and 20 ppt (or PSU)
• Inorganic nitrogen concentrations < 0.4 μM
• Inorganic nitrogen to reactive phosphorus ratios < 5:1
• Elevated water temperatures

While all species of phytoplankton have requirements for phosphorus, blue-green algal species such as Nodularia have the ability to fix atmospheric nitrogen. This is thought to competitively advantage these species when the nitrogen available for other algal species is low.

While low inorganic nitrogen concentrations may lead to blooms of the nitrogen fixing Nodularia, large inputs of inorganic nitrogen (like those that occurred after the 2006/7 bushfires) can trigger blooms of other algal species and were implicated in the bloom of Synechococcus sp. (Cook and Holland 2012).