Caves in the Permian-aged, McCloud Limestone of the Klamath Mountains of Northern California preserve a diverse range of clastic sediments representing broad-scale variations in paleo-hydrologic conditions and transport mechanisms hinting at polygenetic modes of speleogenesis through local landscape development. This study evaluates the polygenetic variability in the distribution, mineralogy, and transport mechanisms of clastic-cave sediments in seven hydrologically-distinct caves in the McCloud Limestone to establish conceptual relationships between clastic-cave sedimentation and speleogenesis. Caves in the McCloud Limestone have developed from approximately 10 to 500 meters above current river base-level and exhibit cave passage geometries and arrangements that suggests periods of both hypogene and epigene cave development through temporal and spatial scales. Many caves exist as relict, dry passages that preserve paleo-hydrologic signatures by the way of well-preserved polygenetic speleogens and clastic sediments. Patterns between the character and distribution of allogenic and autogenic material preserved in hypogene and epigene caves in the McCloud hint at relationships between cave genesis and sedimentation. This study employs a combination of X-ray powder diffraction, laser diffractometer grain-size analysis, and petrographic micromorphology to differentiate depositional conditions, provenance, and hydrologic control on the deposition of clastic material in a set of polygenetic cave environments. Patterns of sedimentary texture and provenance emerged which grouped caves by the paleo-hydrologic controls which transported clastic deposits and interacted with surrounding cave passages. Variability in cave-sediment depositional characteristics have therefore aided in distinguishing paleo-hydrologic conditions between caves and has provided greater insight into the origin of cave genesis in the polygenetic montane karst landscape of the McCloud Limestone of Northern California. Conceptual relationships between cave sedimentation and speleogenesis developed in this study could be applied to other polygenetic karst regions to further the identification of hypogene cave development.