Groundwater levels in basalt aquifers around the world have been declining for many years. Understanding water pathways is needed for solutions like artificial drainage. Water supply in the Palouse Basin, Washington and Idaho, USA, primarily relies on basalt aquifers. This study presents a combination of modeling and field observations to understand the spatial distribution of recharge pathways in the overlying Pleistocene sediments. A spatially distributed model was used to quantify potential recharge rates. The model shows clearly that recharge predominantly occurs through non-argilic soils and soils that are not underlain by fine-grained sediments, i.e. the upper area of the watershed. A field survey was conducted to determine recharge pathways from this area. It revealed 83 perennial springs. Drillings near springs showed connection of coarse-grained layers within the fine-grained Sediments of Bovill to these springs. Such layers, with streambed-like features, act as paleo-channels. Water from one of these coarse-grained layers had a similar electrical conductivity (200 µS cm–1) to water from a downstream perennial spring, also suggesting the existence of a lateral conduit for deep percolation water.