Many Victorian catchments experienced a rainfall‐runoff relationship (RRR) shift during the Millennium Drought (1997–2009). Less annual streamflow was generated from annual rainfall during the drought than would have been expected for the same rainfall before the drought. Changes in weather systems, such as cyclones, fronts, and thunderstorms, were also observed during this period. In this study, we assess the role that changes in weather systems played in the RRR shift. We find that catchments that experienced a RRR shift tended to receive less of their rainfall from frontal weather systems, and more of their rainfall from thunderstorm‐enhanced cyclone and cyclone‐front hybrid systems during the drought than catchments that showed little change in RRR. Overall, changes in the proportion of rainfall from weather systems alone explained up to 43% of the variance in the RRR shift between catchments. Including parameters that quantify catchment processes and physiographic features indicated that weather system changes are not the primary indicator of a RRR shift. Catchment mean slope, aridity and valley confinement, together with proportional rainfall change of cyclone‐thunderstorms and cyclone‐front‐thunderstorms, explained 60% of the variance in the RRR shift between catchments. Focusing on streamflow availability, we find the importance of different weather systems and catchment characteristics varies depending on warm or cool season, eastern or western Victoria, and before or during the drought. Following the drought, some catchments largely maintained the RRR shift that occurred during the drought, and also experienced less of their rainfall from fronts and cyclones compared to the other catchments.