The basin has an overall synclinal structure open to the south at the California boundary where it continues as the Klamath Lake basin in California. The older rocks dip into the basin in monoclinal fashion from the adjoining drainage basins. The rocks are broken along rudely rectangular nets of closely spaced normal faults, the most prominent set of which trends northwest. The network of fault displacements includes two main grabens, the Klamath and the Langell, which were downthrown approximately 500 and 1,000 feet, respectively. The average annual precipitation varies with the altitude, the higher parts of the Cascade Range getting more than 60 inches, and the semiarid valley plains receive as little as 13 inches in some places.
Most precipitation occurs in the winter.
The principal tributaries, Williamson and Sprague Rivers, rise near the higher parts of the eastern rim of the basin, flow through narrow valley plains to the western part, and discharge into Upper Klamath Lake. Wood River and associated creeks also empty into Upper Klamath Lake after draining southward along the eastern foot of the Cascade Range. The Klamath River receives the outflow from Upper Klamath Lake, via Link River and Lake Ewauna, and flows southwestward through Keno Gap and hence through a youthful canyon, to its lower valley in California. The groundwater occurs largely in an unconfined, or water-table, condition, though areas of local confinement are present. The regional water table is graded to a base level about equal to that of the major drainage on the valley plains.