Persistent surface water pools along non-perennial rivers represent an important water resource for plants, animals, and humans. 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 persistent river pools. Here we present an overarching framework for understanding the hydrology of persistent pools. Perched surface water, alluvial water throughflow, and groundwater discharge are the key hydraulic mechanisms that control the persistence of pools along river channels. Groundwater discharge can be further categorized into that controlled by a geological contact or barrier and discharge controlled by topography. Emphasis is put on clearly defining throughflow of alluvial water and the different drivers of groundwater discharge. The suite of regional-scale and pool-scale diagnostic tools available for elucidating these hydraulic mechanisms are summarized and critiqued. Water fluxes to pools supported by throughflow alluvial and groundwater discharge can vary spatially and temporally, and quantitatively resolving pool water balance components is commonly non-trivial. This framework allows for the evaluation of the susceptibility of persistent pools along river channels to changes in climate or groundwater withdrawals. Finally, we demonstrate the application of this framework using a suite of the available tools to conduct a regional and pool-scale assessment of the hydrology of persistent river pools in the Hamersley Basin of north-western Australia.