A persistent puzzle in the study of late Miocene and Pliocene hydrography of the Pacific Northwest United States involves timing and location of connections among the many drainage basins containing sediments and fossils. The Keating, Imbler, and Always Welcome Inn faunas are important datum points that link the Western Snake River Plain to the interior Columbia River Basin. The sites lie in a tectonically active region with punctuated periods of volcanic activity that have periodically disrupted drainage, forcing new connections that allowed faunal interchange between hydrologic basins. Late Miocene to Pliocene fossils from the Keating (Lower Powder), Always Welcome Inn (Baker), and Imbler (Grande Ronde Valley) of northeast Oregon, the Oregon-Idaho Graben and Drewsey-Juntura Graben, Oregon, and lakes of the Western Snake River Plain reveal patterns as well as conflicting evidence. Discovery of distinctive fish groups in the middle Miocene Oregon-Idaho Graben documents the beginning of their appearance in the area following a long period of Oligocene high elevation, cold, and aridity.