Studies of groundwater flow within the Mosier syncline, part of the Yakima Fold Belt, have shown complex flow system boundaries that result from the interaction of Columbia River Basalt Group flows with the paleoenvironment. A developing Mosier syncline provided low areas that hosted drainages and accumulated sediment and controlled the distribution of Saddle Mountains and Wanapum Basalt lava flows of the Columbia River Basalt Group. Those flows interacted with water and water-saturated sediment within the developing syncline to form permeable zones at the flow contacts. Aquifers have been identified in the Pomona Member of the Saddle Mountains Basalt, and in the Priest Rapids and Frenchman Springs Members of the Wanapum Basalt. Units stratigraphically equivalent to the Ellensburg Formation locally form low-permeability sedimentary interbeds within the Columbia River Basalt Group section. Boundary conditions of present groundwater flow systems within Columbia River Basalt Group terrains reflect the stratigraphy and permeability distribution resulting from the depositional environment, and the influences of postdeposition landscape development. Low-permeability boundaries tend to be controlled by stratigraphy and structure. Recharge and discharge boundaries tend to result from postdepositional landscape development such as changes in topography and drainage systems. Analysis of hydrologic information provides insights into the influences of stresses and boundaries on Columbia River Basalt Group groundwater systems. Hydraulic head data have shown that the main stresses to the flow system near Mosier are pumping, interaquifer flow through uncased wells, and climate fluctuations. Long-term groundwater declines are the result of overpumping in the Pomona aquifer and depressurization of other aquifers connected to the Pomona aquifer through uncased wells. The groundwater system discharges to Mosier Creek, and the elevation of the discharge point appears to control the lower limit of observed heads throughout the aquifer system.

Neogene sedimentation on and adjacent to the Columbia Plateau in Oregon, Washington, and Idaho was related to volcanism and tectonism. During emplacement of the largest volume of middle Miocene flood basalts (Grande Ronde, Picture Gorge, and Wanapum Basalts), local drainage disruption and gradient diminishment caused deposition in lakes and by sluggish mixed-load streams at or near the flow margins (e.g., Latah, lower Ellensburg, and Simtustus Formations). The Pasco basin was the principal subsiding feature at this time, but because of its central position on the basalt plateau, it received only minor accumulations of detrital and organic-rich sediments. The Mascall and Payette Formations (and equivalents) were deposited in subsiding basins along the southern and southeastern plateau margins. As basalt eruptive frequency and volume diminished in late Miocene time (Saddle Mountains Basalt), deposition occurred primarily in response to intrabasin tectonism and Cascade volcanism. A well-integrated through-flowing river system transported detritus from the surrounding highlands across the plateau. Late Miocene sedimentation along the western plateau margin was strongly influenced by large volcaniclastic sediment loads from the Cascade Range (upper Ellensburg, Dalles, and Deschutes Formations). Elsewhere, fluvial and lacustrine deposition occurred in response to basin subsidence (e.g., Ringold and Idaho Formations) or influx of coarse clastics into shallow basins (e.g., Alkali Canyon and McKay Formations, Thorp Gravel). Widespread unconformities and provenances indicative of drainage reversals in the Blue Mountains region may reflect a transition from primarily compressional to extensional deformation along the southern margin of the plateau between 12 and 10 Ma.