This paper presents a systematic examination of the process controls on inter-annual variability of annual water balance. A simple, linear rainfall–runoff model is used for this purpose, in combination with idealised patterns of within-year variability of rainfall. The effects of these intra-annual patterns of variability of climate (e.g., storminess, seasonality) on annual water balance are examined through the simulation of annual runoff in three semi-arid catchments located in Queensland, South Australia and Western Australia, and one temperate catchment in New Zealand. A simple lumped model, that includes saturation excess overland flow and subsurface stormflow, is used, via sensitivity analyses with respect to different aspects of the intra-annual variability (i.e., seasonality and storminess). In the Queensland catchment storminess is found to be the dominant factor, whereas in Western Australia and South Australia seasonality is found to be the dominant climate control. In wetter catchments (e.g., New Zealand), the water balance is relatively insensitive to soil properties, whereas in dry places (e.g., Western Australia and South Australia) the water balance is highly sensitive to soil properties, such as the soil depth, confirming the results of previous modelling studies. The insights gained from this study can assist in the deciphering of the vast complexity of observed inter-annual variability of catchment responses in terms of their underlying process controls, which can be valuable towards the development of parsimonious water balance models.