This study focused on diagnosing the relative and independent role of El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) on austral cool seasonal rainfall by stratifying the cool seasonal rainfall into winter (June–August) and spring (September–November). Partial regression and classification analysis was used to investigate the effect of the climate modes on rainfall in the state of Victoria in southeast Australia. Partial regression analyses revealed that when the influence of IOD is removed from ENSO, sea surface temperature (SST) anomalies in the Pacific Ocean have no significant effect on spring rainfall across Victoria and affect winter rainfall mildly in west Victoria. By removing the inter-correlations between ENSO and IOD, SST anomalies in the Indian Ocean and SLP anomalies in the Pacific Ocean showed weak relationships with Victoria's spring and winter rainfall. Classification analysis demonstrated the effects of phases of ENSO and IOD on Victoria's seasonal rainfall; the dry phases of the climate modes have more effect on spring rainfall compared to the wet phases and both show no significant effect on winter rainfalls. It is recommended that for water availability forecasting in Victoria, water managers should focus on the effect of climate modes on spring rainfalls, particularly during the dry phases of ENSO and IOD.