During Phase I of the project "Assessment of Ecological Risk Associated with Irrigation Systems in the Goulburn Broken Catchment" (Cottingham et al., 2001) adverse changes to the abundance and diversity of native fish and the occurrence of cyanobacterial (or blue-green algal) blooms were identified as priority ecological issues to be further investigated in Phase II of the project. Investigations have now been carried out to further assess the risks associated with these two issues.