From the late Miocene to the middle Pliocene, the current drainage basin of the Owens River probably consisted of a broad, moderate-elevation, low-relief plateau with radiating drainage toward the Pacific Ocean, the northwestern Great Basin (now Lahontan drainages), and the Mojave and Colorado drainages. This plateau probably contained shallow basins, created by an extensional pulse at 12–11 Ma, at the present locations of major valleys. Between 4 and 3 Ma, this plateau was disrupted by a rapid westward step of extensional Basin and Range Province tectonism, which reactivated the Miocene faults and resulted in a linear north-south valley (the Owens Valley) with high mountain ranges on each side. This tectonic event resulted in geographic isolation and fragmentation of aquatic habitats and may have been a critical driver for speciation of aquatic organisms. Subsequent to this remarkable transformation of the landscape, the predominant influence on aquatic habitats has been very large, climate-driven fluctuations in the regional water balance that have resulted in the repeated interconnection and disconnection of the various basins that make up the paleo–Owens system. The magnitude of these fluctuations appears to have increased markedly since the early Pleistocene. Searles Lake has generally been the terminus of the Owens River, but at least once, probably at ca. 150 and/or ca. 70 ka, the system overflowed into Death Valley. During the last interglacial (marine isotope stage 5) and the Holocene, Owens Lake has been the terminus, but apparently not frequently before. These very large fluctuations in the water balance undoubtedly produced large shifts in the nature and distribution of aquatic habitats over geologically short periods of time, as well as repeatedly creating and severing connections between various parts of the larger drainage basin. This dynamic hydrological system provided the setting, and no doubt much of the impetus, for speciation, extinction, and distribution of aquatic species within the paleo–Owens system, but any paleohydrological causes will have to be extracted from a complex history.