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Arid and semi-arid regions experience large hydroclimatic variability and decadal-scale droughts. During droughts, the reduced water availability alters the biophysical properties of the catchments which leads to non-stationarity in rainfall-runoff (r-r) relationships. Uncertainty exists regarding the mechanisms causing r-r non-stationarity, especially at seasonal scales. This study analyses endogenous and exogenous catchment mechanisms which could possibly influence r-r relationships in two case study catchments in southeast Australia (SEA). The case study catchments are chosen such that they are representative of arid to semi-arid catchments that experience large climatic variability and decadal-scale droughts. The results demonstrate that endogenous catchment mechanisms (i.e. groundwater table, baseflow and vegetation) have stronger influences on non-stationarity in r-r relationships than exogenous catchment mechanisms like temperature and potential evapo-transpiration. These findings highlight the importance of understanding changes in r-r relationships in order to develop more realistic and reliable hydrological models that are needed to quantify and adapt to the impacts of changing catchment or hydroclimatic conditions. While this study is focussed on SEA the findings are relevant to all catchments that experience large climatic variability and decadal-scale droughts.