Abstract Neogene drainage development in southeastern Idaho has been influenced by drainage capture, Basin and Range faulting, volcanism, and the Late Pleistocene Lake Bonneville overflow and Bonneville Flood. In Marsh Valley, the Middle to Late Pleistocene sedimentary sequence is dominated by alternating lacustrine/paludal and alluvial sediments, which have yielded new 40Ar/39Ar, amino acid racemization, and luminescence age estimates. The pattern of sedimentation through time indicates poor drainage integration of southern Marsh Valley through most of the last ca. 640 ka and suggests slow basin subsidence along Quaternary faults mapped on the basin edges. Marsh Valley initially incised into that valley fill sequence ca. 19 ka, shortly before the Bonneville Flood. Marsh Creek is a markedly underfit stream occupying a meandering, broad valley carved into the valley fill sequence. These geomorphic and sedimentologic patterns suggest non-catastrophic Lake Bonneville overflow before and after the Bonneville Flood. In Portneuf Valley, ca. 8.5–7.4 Ma basin fill and a bedrock pediment are perched 800 m above the modern valley floor. Major incision of basin fill and bedrock by the ancestral Portneuf drainage system occurred prior to the Middle to Late Pleistocene, when two cut-fill events resulted in accumulation of alluvial fan deposits extending ~10–60 m above the modern valley floor and basalt extending ~10 m below to 20 m above the modern valley floor. Final incision by Lake Bonneville overflow is evident but relatively minor in comparison to the cumulative downcutting. Overall, incision is attributed to isostatic subsidence of the eastern Snake River Plain, which served as base level for the Portneuf drainage system after passage of the Yellowstone hot spot in late Miocene time.