Abstract. Persistent surface water pools along non-perennial rivers represent an important water resource for the plants, animals, and humans that inhabit semi-arid regions. While ecological studies of these features are not uncommon, these are rarely accompanied by a rigorous examination of the hydrological and hydrogeological characteristics that create or support the pools. Here we present an overarching framework for understanding the hydrology of persistent pools based on data from 22 pools in the Hamersley Basin in Western Australia. Three dominant mechanisms that control the occurrence of persistent pools have been identified; perched pools, through flow pools and groundwater discharge pools. Groundwater discharge pools are further categorized into those that are present because of a geological contact or barrier, and those that are controlled by topography. A suite of diagnostic tools (including geological mapping, hydraulic data and hydrochemical surveys) is generally required to identify the mechanism supporting persistent pools. Perched pools are sensitive to climate variability but their persistence is largely independent of groundwater withdrawals. Water fluxes to pools from alluvial and bedrock aquifers can vary seasonally and resolving these inputs is generally non-trivial. The susceptibility of through-flow and groundwater discharge pools to climate variations and groundwater withdrawals depends on the mechanism of pool persistence and the spatial distribution of stressors relative to the pool. Although this framework was developed in the context of north-western Australia, this framework can also be applied to pools and springs found along non-perennial rivers around the world.