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.

Maps of the distribution of Middle Proterozoic through Cretaceous rocks beneath the Tertiary unconformities in eastern Idaho effectively remove differential uplift associated with Basin and Range tectonism and reveal preextensional structural relief associated with folds and thrusts in the western part of the Idaho-Wyoming-Montana thrust belt. North of the Snake River Plain, the paleogeologic map shows that regionally extensive Middle Proterozoic to Triassic strata and the Cretaceous Idaho batholith were variably uplifted and exposed prior to formation of the Eocene Challis volcanic field. In the Beaverhead Mountains, Ordovician and Triassic strata are juxtaposed along the Hawley Creek thrust. In the northern Lemhi and Lost River ranges, west- and south-dipping homoclines beneath the Eocene unconformity are interpreted to reflect folding above frontal and lateral ramps in the footwall of the Hawley Creek thrust system. In the southern Lemhi and Lost River ranges, the White Knob Mountains, and eastern Pioneer Mountains, Mississippian to Permian strata underlie most of the unconformity. Stratigraphic offset is evident along the exposed Pioneer and Copper Basin thrust faults, but along the exposed Glide Mountain thrust as well as the concealed White Knob, Grouse, and Lost River-Arco Hills thrusts uplift was insufficient to juxtapose rocks of different systems. To the west, the Idaho batholith and Pennsylvanian-Permian rocks are juxtaposed beneath the Eocene unconformity. Several kilometers of overburden covered both the batholith and Permian rocks in Cretaceous time and were regionally eroded prior to extrusion of Eocene volcanic rocks. South of the Snake River Plain and west of the exposed traces of the Paris and Putnam thrust faults, Late Proterozoic to Permian strata unconformably underlie Miocene sedimentary and volcanic rocks. The Paris thrust separates Late Proterozoic through Mississippian strata in its hanging wall from Pennsylvanian through Triassic rocks in its footwall, and the Putnam thrust separates Late Proterozoic to Ordovician strata from Pennsylvanian to Triassic strata. Beneath the unconformity, stratigraphic displacement appears to diminish northwestward along the Paris thrust and southeastward along the Putnam thrust, supporting the interpretation that displacement is progressively transferred from one thrust to the other. Lower Paleozoic strata generally underlie the unconformity between the emergent thrust system and the Arbon and Malad valleys. West of these valleys, Pennsylvanian-Permian strata everywhere underlie the unconformity. A simple flat-ramp-flat-thrust fault geometry of the Paris-Putnam thrust system may explain the outcrop pattern, with hanging-wall and footwall flats beneath the regions of low structural relief, separated by a footwall ramp located beneath the modern Malad and Arbon valleys. Paleogeologic maps show that the Paris-Putnam thrust sheet was probably not an important source of quartzose clasts in the Cretaceous-Tertiary Harebell and Pinyon formations of northwest Wyoming.