As global population increases and climates shift, intermittent rivers and ephemeral streams (IRES) are receiving increased attention from researchers and water resource managers. These types of systems are commonly associated with arid regions of the world, but are also present in temperate Mediterranean-type climates. While the distinction between IRES and perennial systems can be useful, not all streams or rivers neatly into one of these categories. Here we present two examples of streams in different climates that have both ephemeral and perennial flow regimes along their length. Longitudinal stream surveys, groundwater monitoring and geophysical mapping identified that in both cases the underlying geology is the key control on the surface water flow regime. The first site is the Donnelly River in south-west Western Australia (WA). The Donnelly River flows across the deeply weathered granite of the Yilgarn Craton and onto the unconsolidated alluvial sediments of the Scott Coastal Plain (SCP). Decreasing rainfall has resulted in a change from perennial to ephemeral flow over the Yilgarn Craton, but our data demonstrate that groundwater discharge across the geological transition to the SCP still maintains perennial flow along the lower reaches of the river. The second site, Spring Creek, is located on the Dampier Peninsula in the Kimberley region of northern WA. The headwaters coincide with perennial groundwater springs, below which we identified a sequence of perennial and ephemeral reaches on the order of 10 km in length. Geophysical surveys identified a previously un-mapped confining layer that results in the “pinching out” of the upper Broome Sandstone aquifer. This geological transition causes groundwater discharge that maintains stream flow along the perennial reaches of the stream. These two examples from varying climates highlight the importance of geological controls on stream flow generation in intermittent and ephemeral stream systems. This type of process-based understanding of stream flow generation is critical to ensure appropriate monitoring and management of IRES under threat from changing climate or increased water use.