Abstract. There is a growing interest globally in the spatial distribution of intermittently flowing streams and rivers, and how their spatial extent varies in relation to climatic factors. However, deriving consistent information on the extent of flow intermittency within river networks is hampered by the fact that streamflow gauges are often sparsely distributed and more often located within the most perennial parts of the river network. Here, we developed an approach to quantify catchment-wide streamflow intermittency over long timeframes and in a spatially explicit manner, using readily accessible and spatially contiguous daily runoff data from a national-scale water balance model. We examined the ability of the water balance model to simulate streamflow in two hydro-climatically distinctive (subtropical and temperate) regions in Australia, with a particular focus on low flow simulations. We also evaluated the effect of model time step (daily vs. monthly) on flow intermittency estimation to inform future model selection. The water balance model showed better performance in the temperate region characterised by steady baseflow than in the subtropical region with flashy hydrographs and frequent cease-to-flow periods. The model tended to overestimate low flow magnitude due to both overestimation of gains (e.g. groundwater release to baseflow) and underestimation of losses (e.g. transmission losses) during low-flow periods. Modelled patterns of flow intermittency revealed highly dynamic behaviour in space and time, with intermittent flows affecting between 29 % and 80 % of the river network over the period of 1911–2016. The daily flow model did not perform better than the monthly flow model in quantifying flow intermittency, and model selection should depend on the intended application of the model outputs. Our general approach to quantifying spatio-temporal patterns of flow intermittency is transferable to other parts of the world, and can inform hydro-ecological understanding and management of intermittent streams where limited gauging data are available.