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.